diff --git a/00/00_Data_Overview_and_Preparation_Sample_Data.ipynb b/00/00_Data_Overview_and_Preparation_Sample_Data.ipynb index 146dee0..1ec3bea 100644 --- a/00/00_Data_Overview_and_Preparation_Sample_Data.ipynb +++ b/00/00_Data_Overview_and_Preparation_Sample_Data.ipynb @@ -1065,67 +1065,6 @@ "nrow(sample_data) # more because some samples measured twice" ] }, - { - "cell_type": "code", - "execution_count": 47, - "id": "ff9f0251-8536-47a1-a446-81f0ed509fc9", - "metadata": {}, - "outputs": [ - { - "data": { - "text/html": [ - "\n", - "\n", - "\n", - "\t\n", - "\t\n", - "\n", - "\n", - "\t\n", - "\t\n", - "\n", - "
A data.frame: 2 × 15
idsamplemeasurementsample_idlibraryid.ynamereadpatternsequencefeature_typeXin_samplemeasurement_tpsc_rna_seq_data
<chr><chr><chr><chr><chr><chr><chr><chr><chr><chr><chr><lgl><int><chr><dbl>
11 K1TP0k1 L13HTO_B0251No-CCS-1R25PNNNNNNNNNN(BC)GTCAACTCTTTAGCGAntibody CaptureNA0No-CCS1
21.1M1TP1m1.1L1 HTO_B02511.1 R25PNNNNNNNNNN(BC)GTCAACTCTTTAGCGAntibody CaptureNA1TP1 1
\n" - ], - "text/latex": [ - "A data.frame: 2 × 15\n", - "\\begin{tabular}{r|lllllllllllllll}\n", - " & id & sample & measurement & sample\\_id & library & id.y & name & read & pattern & sequence & feature\\_type & X & in\\_sample & measurement\\_tp & sc\\_rna\\_seq\\_data\\\\\n", - " & & & & & & & & & & & & & & & \\\\\n", - "\\hline\n", - "\t1 & 1 & K1 & TP0 & k1 & L13 & HTO\\_B0251 & No-CCS-1 & R2 & 5PNNNNNNNNNN(BC) & GTCAACTCTTTAGCG & Antibody Capture & NA & 0 & No-CCS & 1\\\\\n", - "\t2 & 1.1 & M1 & TP1 & m1.1 & L1 & HTO\\_B0251 & 1.1 & R2 & 5PNNNNNNNNNN(BC) & GTCAACTCTTTAGCG & Antibody Capture & NA & 1 & TP1 & 1\\\\\n", - "\\end{tabular}\n" - ], - "text/markdown": [ - "\n", - "A data.frame: 2 × 15\n", - "\n", - "| | id <chr> | sample <chr> | measurement <chr> | sample_id <chr> | library <chr> | id.y <chr> | name <chr> | read <chr> | pattern <chr> | sequence <chr> | feature_type <chr> | X <lgl> | in_sample <int> | measurement_tp <chr> | sc_rna_seq_data <dbl> |\n", - "|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|\n", - "| 1 | 1 | K1 | TP0 | k1 | L13 | HTO_B0251 | No-CCS-1 | R2 | 5PNNNNNNNNNN(BC) | GTCAACTCTTTAGCG | Antibody Capture | NA | 0 | No-CCS | 1 |\n", - "| 2 | 1.1 | M1 | TP1 | m1.1 | L1 | HTO_B0251 | 1.1 | R2 | 5PNNNNNNNNNN(BC) | GTCAACTCTTTAGCG | Antibody Capture | NA | 1 | TP1 | 1 |\n", - "\n" - ], - "text/plain": [ - " id sample measurement sample_id library id.y name read\n", - "1 1 K1 TP0 k1 L13 HTO_B0251 No-CCS-1 R2 \n", - "2 1.1 M1 TP1 m1.1 L1 HTO_B0251 1.1 R2 \n", - " pattern sequence feature_type X in_sample measurement_tp\n", - "1 5PNNNNNNNNNN(BC) GTCAACTCTTTAGCG Antibody Capture NA 0 No-CCS \n", - "2 5PNNNNNNNNNN(BC) GTCAACTCTTTAGCG Antibody Capture NA 1 TP1 \n", - " sc_rna_seq_data\n", - "1 1 \n", - "2 1 " - ] - }, - "metadata": {}, - "output_type": "display_data" - } - ], - "source": [ - "head(sample_data,2)" - ] - }, { "cell_type": "code", "execution_count": 48, @@ -1380,64 +1319,6 @@ "group_classification$library = paste0('L', str_replace(group_classification$library.hashtag, '\\\\..*', ''))" ] }, - { - "cell_type": "code", - "execution_count": 57, - "id": "cb5d2fd2-bf11-4580-b9c1-e716cfb9cc7c", - "metadata": {}, - "outputs": [ - { - "data": { - "text/html": [ - "\n", - "\n", - "\n", - "\t\n", - "\t\n", - "\n", - "\n", - "\t\n", - "\t\n", - "\n", - "
A data.frame: 2 × 9
library.hashtagagesexmclassificationgroupmeasurementsamplelibrary
<dbl><int><chr><chr><chr><chr><chr><chr><chr>
1 NA55fK1vollstaendiger_ausschlussno_ccsTP01 LNA
21.262mM2acs_w_o_infection acs TP12.1L1
\n" - ], - "text/latex": [ - "A data.frame: 2 × 9\n", - "\\begin{tabular}{r|lllllllll}\n", - " & library.hashtag & age & sex & m & classification & group & measurement & sample & library\\\\\n", - " & & & & & & & & & \\\\\n", - "\\hline\n", - "\t1 & NA & 55 & f & K1 & vollstaendiger\\_ausschluss & no\\_ccs & TP0 & 1 & LNA\\\\\n", - "\t2 & 1.2 & 62 & m & M2 & acs\\_w\\_o\\_infection & acs & TP1 & 2.1 & L1 \\\\\n", - "\\end{tabular}\n" - ], - "text/markdown": [ - "\n", - "A data.frame: 2 × 9\n", - "\n", - "| | library.hashtag <dbl> | age <int> | sex <chr> | m <chr> | classification <chr> | group <chr> | measurement <chr> | sample <chr> | library <chr> |\n", - "|---|---|---|---|---|---|---|---|---|---|\n", - "| 1 | NA | 55 | f | K1 | vollstaendiger_ausschluss | no_ccs | TP0 | 1 | LNA |\n", - "| 2 | 1.2 | 62 | m | M2 | acs_w_o_infection | acs | TP1 | 2.1 | L1 |\n", - "\n" - ], - "text/plain": [ - " library.hashtag age sex m classification group measurement\n", - "1 NA 55 f K1 vollstaendiger_ausschluss no_ccs TP0 \n", - "2 1.2 62 m M2 acs_w_o_infection acs TP1 \n", - " sample library\n", - "1 1 LNA \n", - "2 2.1 L1 " - ] - }, - "metadata": {}, - "output_type": "display_data" - } - ], - "source": [ - "head(group_classification,2)" - ] - }, { "cell_type": "code", "execution_count": 58, @@ -1477,61 +1358,6 @@ "classification_data = unique(group_classification[,c('age', 'sex', 'm', 'classification', 'group')])" ] }, - { - "cell_type": "code", - "execution_count": 60, - "id": "3f8b2843-0fbf-44d6-bae0-e5453deb82f9", - "metadata": {}, - "outputs": [ - { - "data": { - "text/html": [ - "\n", - "\n", - "\n", - "\t\n", - "\t\n", - "\n", - "\n", - "\t\n", - "\t\n", - "\n", - "
A data.frame: 2 × 5
agesexmclassificationgroup
<int><chr><chr><chr><chr>
155fK1vollstaendiger_ausschlussno_ccs
262mM2acs_w_o_infection acs
\n" - ], - "text/latex": [ - "A data.frame: 2 × 5\n", - "\\begin{tabular}{r|lllll}\n", - " & age & sex & m & classification & group\\\\\n", - " & & & & & \\\\\n", - "\\hline\n", - "\t1 & 55 & f & K1 & vollstaendiger\\_ausschluss & no\\_ccs\\\\\n", - "\t2 & 62 & m & M2 & acs\\_w\\_o\\_infection & acs \\\\\n", - "\\end{tabular}\n" - ], - "text/markdown": [ - "\n", - "A data.frame: 2 × 5\n", - "\n", - "| | age <int> | sex <chr> | m <chr> | classification <chr> | group <chr> |\n", - "|---|---|---|---|---|---|\n", - "| 1 | 55 | f | K1 | vollstaendiger_ausschluss | no_ccs |\n", - "| 2 | 62 | m | M2 | acs_w_o_infection | acs |\n", - "\n" - ], - "text/plain": [ - " age sex m classification group \n", - "1 55 f K1 vollstaendiger_ausschluss no_ccs\n", - "2 62 m M2 acs_w_o_infection acs " - ] - }, - "metadata": {}, - "output_type": "display_data" - } - ], - "source": [ - "head(classification_data,2)" - ] - }, { "cell_type": "code", "execution_count": 61, @@ -1691,64 +1517,6 @@ "all_samples_info = merge(all_samples_info, classification_data, by.x = 'sample', by.y = 'm', all.x = TRUE)" ] }, - { - "cell_type": "code", - "execution_count": 70, - "id": "1b53aee8-3997-49e0-8c6c-e45bedf27566", - "metadata": {}, - "outputs": [ - { - "data": { - "text/html": [ - "\n", - "\n", - "\n", - "\t\n", - "\t\n", - "\n", - "\n", - "\t\n", - "\t\n", - "\n", - "
A data.frame: 2 × 10
sampleidmeasurementsample_idsc_rna_seq_dataagesexclassificationgroupmeta_data
<chr><chr><chr><chr><dbl><int><chr><chr><chr><dbl>
1K1 1 TP0k1 055fvollstaendiger_ausschlussno_ccs1
2K1010TP0k10157mccs ccs 1
\n" - ], - "text/latex": [ - "A data.frame: 2 × 10\n", - "\\begin{tabular}{r|llllllllll}\n", - " & sample & id & measurement & sample\\_id & sc\\_rna\\_seq\\_data & age & sex & classification & group & meta\\_data\\\\\n", - " & & & & & & & & & & \\\\\n", - "\\hline\n", - "\t1 & K1 & 1 & TP0 & k1 & 0 & 55 & f & vollstaendiger\\_ausschluss & no\\_ccs & 1\\\\\n", - "\t2 & K10 & 10 & TP0 & k10 & 1 & 57 & m & ccs & ccs & 1\\\\\n", - "\\end{tabular}\n" - ], - "text/markdown": [ - "\n", - "A data.frame: 2 × 10\n", - "\n", - "| | sample <chr> | id <chr> | measurement <chr> | sample_id <chr> | sc_rna_seq_data <dbl> | age <int> | sex <chr> | classification <chr> | group <chr> | meta_data <dbl> |\n", - "|---|---|---|---|---|---|---|---|---|---|---|\n", - "| 1 | K1 | 1 | TP0 | k1 | 0 | 55 | f | vollstaendiger_ausschluss | no_ccs | 1 |\n", - "| 2 | K10 | 10 | TP0 | k10 | 1 | 57 | m | ccs | ccs | 1 |\n", - "\n" - ], - "text/plain": [ - " sample id measurement sample_id sc_rna_seq_data age sex\n", - "1 K1 1 TP0 k1 0 55 f \n", - "2 K10 10 TP0 k10 1 57 m \n", - " classification group meta_data\n", - "1 vollstaendiger_ausschluss no_ccs 1 \n", - "2 ccs ccs 1 " - ] - }, - "metadata": {}, - "output_type": "display_data" - } - ], - "source": [ - "head(all_samples_info,2)" - ] - }, { "cell_type": "code", "execution_count": 71, @@ -1856,67 +1624,6 @@ "nrow(sample_data)" ] }, - { - "cell_type": "code", - "execution_count": 76, - "id": "802aee1e-fa1e-4d74-9f8d-189ca3828847", - "metadata": {}, - "outputs": [ - { - "data": { - "text/html": [ - "\n", - "\n", - "\n", - "\t\n", - "\t\n", - "\n", - "\n", - "\t\n", - "\t\n", - "\n", - "
A data.frame: 2 × 15
idsamplemeasurementsample_idlibraryid.ynamereadpatternsequencefeature_typeXin_samplemeasurement_tpsc_rna_seq_data
<chr><chr><chr><chr><chr><chr><chr><chr><chr><chr><chr><lgl><int><chr><dbl>
11 K1TP0k1 L13HTO_B0251No-CCS-1R25PNNNNNNNNNN(BC)GTCAACTCTTTAGCGAntibody CaptureNA0No-CCS1
21.1M1TP1m1.1L1 HTO_B02511.1 R25PNNNNNNNNNN(BC)GTCAACTCTTTAGCGAntibody CaptureNA1TP1 1
\n" - ], - "text/latex": [ - "A data.frame: 2 × 15\n", - "\\begin{tabular}{r|lllllllllllllll}\n", - " & id & sample & measurement & sample\\_id & library & id.y & name & read & pattern & sequence & feature\\_type & X & in\\_sample & measurement\\_tp & sc\\_rna\\_seq\\_data\\\\\n", - " & & & & & & & & & & & & & & & \\\\\n", - "\\hline\n", - "\t1 & 1 & K1 & TP0 & k1 & L13 & HTO\\_B0251 & No-CCS-1 & R2 & 5PNNNNNNNNNN(BC) & GTCAACTCTTTAGCG & Antibody Capture & NA & 0 & No-CCS & 1\\\\\n", - "\t2 & 1.1 & M1 & TP1 & m1.1 & L1 & HTO\\_B0251 & 1.1 & R2 & 5PNNNNNNNNNN(BC) & GTCAACTCTTTAGCG & Antibody Capture & NA & 1 & TP1 & 1\\\\\n", - "\\end{tabular}\n" - ], - "text/markdown": [ - "\n", - "A data.frame: 2 × 15\n", - "\n", - "| | id <chr> | sample <chr> | measurement <chr> | sample_id <chr> | library <chr> | id.y <chr> | name <chr> | read <chr> | pattern <chr> | sequence <chr> | feature_type <chr> | X <lgl> | in_sample <int> | measurement_tp <chr> | sc_rna_seq_data <dbl> |\n", - "|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|\n", - "| 1 | 1 | K1 | TP0 | k1 | L13 | HTO_B0251 | No-CCS-1 | R2 | 5PNNNNNNNNNN(BC) | GTCAACTCTTTAGCG | Antibody Capture | NA | 0 | No-CCS | 1 |\n", - "| 2 | 1.1 | M1 | TP1 | m1.1 | L1 | HTO_B0251 | 1.1 | R2 | 5PNNNNNNNNNN(BC) | GTCAACTCTTTAGCG | Antibody Capture | NA | 1 | TP1 | 1 |\n", - "\n" - ], - "text/plain": [ - " id sample measurement sample_id library id.y name read\n", - "1 1 K1 TP0 k1 L13 HTO_B0251 No-CCS-1 R2 \n", - "2 1.1 M1 TP1 m1.1 L1 HTO_B0251 1.1 R2 \n", - " pattern sequence feature_type X in_sample measurement_tp\n", - "1 5PNNNNNNNNNN(BC) GTCAACTCTTTAGCG Antibody Capture NA 0 No-CCS \n", - "2 5PNNNNNNNNNN(BC) GTCAACTCTTTAGCG Antibody Capture NA 1 TP1 \n", - " sc_rna_seq_data\n", - "1 1 \n", - "2 1 " - ] - }, - "metadata": {}, - "output_type": "display_data" - } - ], - "source": [ - "head(sample_data,2)" - ] - }, { "cell_type": "code", "execution_count": 77, @@ -1956,69 +1663,6 @@ "nrow(sample_data)" ] }, - { - "cell_type": "code", - "execution_count": 79, - "id": "068aa3a6-d2f4-43ca-973c-225781fe3328", - "metadata": { - "tags": [] - }, - "outputs": [ - { - "data": { - "text/html": [ - "\n", - "\n", - "\n", - "\t\n", - "\t\n", - "\n", - "\n", - "\t\n", - "\t\n", - "\n", - "
A data.frame: 2 × 20
sampleidmeasurementsample_idlibraryid.ynamereadpatternsequencefeature_typeXin_samplemeasurement_tpsc_rna_seq_dataagesexclassificationgroupmeta_data
<chr><chr><chr><chr><chr><chr><chr><chr><chr><chr><chr><lgl><int><chr><dbl><int><chr><chr><chr><dbl>
1K1 1 TP0k1 L13HTO_B0251No-CCS-1 R25PNNNNNNNNNN(BC)GTCAACTCTTTAGCGAntibody CaptureNA0No-CCS 155fvollstaendiger_ausschlussno_ccs1
2K1010TP0k10L11HTO_B0256Ch-CCS-10R25PNNNNNNNNNN(BC)GGTTGCCAGATGTCAAntibody CaptureNA1Chronic-CCS157mccs ccs 1
\n" - ], - "text/latex": [ - "A data.frame: 2 × 20\n", - "\\begin{tabular}{r|llllllllllllllllllll}\n", - " & sample & id & measurement & sample\\_id & library & id.y & name & read & pattern & sequence & feature\\_type & X & in\\_sample & measurement\\_tp & sc\\_rna\\_seq\\_data & age & sex & classification & group & meta\\_data\\\\\n", - " & & & & & & & & & & & & & & & & & & & & \\\\\n", - "\\hline\n", - "\t1 & K1 & 1 & TP0 & k1 & L13 & HTO\\_B0251 & No-CCS-1 & R2 & 5PNNNNNNNNNN(BC) & GTCAACTCTTTAGCG & Antibody Capture & NA & 0 & No-CCS & 1 & 55 & f & vollstaendiger\\_ausschluss & no\\_ccs & 1\\\\\n", - "\t2 & K10 & 10 & TP0 & k10 & L11 & HTO\\_B0256 & Ch-CCS-10 & R2 & 5PNNNNNNNNNN(BC) & GGTTGCCAGATGTCA & Antibody Capture & NA & 1 & Chronic-CCS & 1 & 57 & m & ccs & ccs & 1\\\\\n", - "\\end{tabular}\n" - ], - "text/markdown": [ - "\n", - "A data.frame: 2 × 20\n", - "\n", - "| | sample <chr> | id <chr> | measurement <chr> | sample_id <chr> | library <chr> | id.y <chr> | name <chr> | read <chr> | pattern <chr> | sequence <chr> | feature_type <chr> | X <lgl> | in_sample <int> | measurement_tp <chr> | sc_rna_seq_data <dbl> | age <int> | sex <chr> | classification <chr> | group <chr> | meta_data <dbl> |\n", - "|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|\n", - "| 1 | K1 | 1 | TP0 | k1 | L13 | HTO_B0251 | No-CCS-1 | R2 | 5PNNNNNNNNNN(BC) | GTCAACTCTTTAGCG | Antibody Capture | NA | 0 | No-CCS | 1 | 55 | f | vollstaendiger_ausschluss | no_ccs | 1 |\n", - "| 2 | K10 | 10 | TP0 | k10 | L11 | HTO_B0256 | Ch-CCS-10 | R2 | 5PNNNNNNNNNN(BC) | GGTTGCCAGATGTCA | Antibody Capture | NA | 1 | Chronic-CCS | 1 | 57 | m | ccs | ccs | 1 |\n", - "\n" - ], - "text/plain": [ - " sample id measurement sample_id library id.y name read\n", - "1 K1 1 TP0 k1 L13 HTO_B0251 No-CCS-1 R2 \n", - "2 K10 10 TP0 k10 L11 HTO_B0256 Ch-CCS-10 R2 \n", - " pattern sequence feature_type X in_sample measurement_tp\n", - "1 5PNNNNNNNNNN(BC) GTCAACTCTTTAGCG Antibody Capture NA 0 No-CCS \n", - "2 5PNNNNNNNNNN(BC) GGTTGCCAGATGTCA Antibody Capture NA 1 Chronic-CCS \n", - " sc_rna_seq_data age sex classification group meta_data\n", - "1 1 55 f vollstaendiger_ausschluss no_ccs 1 \n", - "2 1 57 m ccs ccs 1 " - ] - }, - "metadata": {}, - "output_type": "display_data" - } - ], - "source": [ - "head(sample_data,2)" - ] - }, { "cell_type": "raw", "id": "6dad6bc9-91f0-4bae-82ba-58e1668490ff", @@ -2067,54 +1711,38 @@ }, { "cell_type": "code", - "execution_count": 82, - "id": "ecda4595-82df-427d-be5c-1de2a0baacf8", - "metadata": { - "tags": [] - }, + "execution_count": 83, + "id": "1180f3c3-6a12-44ec-b32a-1a9af5e69748", + "metadata": {}, "outputs": [ { "data": { "text/html": [ - "\n", - "\n", - "\n", - "\t\n", - "\t\n", - "\n", - "\n", - "\t\n", - "\t\n", - "\n", - "
A data.frame: 2 × 7
Xlibrary.hashtagmmeasurementdelta_ef_value_groupdelta_ef_valuesample
<int><chr><chr><chr><chr><dbl><chr>
111.2M2 (1,15) TP1x_greater_11.152.1
221.4M4 (3,1) TP1x_greater_13.104.1
\n" + "\n", + "
  1. 'x_greater_1'
  2. 'x_smaller_1'
  3. 'x_smaller_0'
  4. NA
\n" ], "text/latex": [ - "A data.frame: 2 × 7\n", - "\\begin{tabular}{r|lllllll}\n", - " & X & library.hashtag & m & measurement & delta\\_ef\\_value\\_group & delta\\_ef\\_value & sample\\\\\n", - " & & & & & & & \\\\\n", - "\\hline\n", - "\t1 & 1 & 1.2 & M2 (1,15) & TP1 & x\\_greater\\_1 & 1.15 & 2.1\\\\\n", - "\t2 & 2 & 1.4 & M4 (3,1) & TP1 & x\\_greater\\_1 & 3.10 & 4.1\\\\\n", - "\\end{tabular}\n" + "\\begin{enumerate*}\n", + "\\item 'x\\_greater\\_1'\n", + "\\item 'x\\_smaller\\_1'\n", + "\\item 'x\\_smaller\\_0'\n", + "\\item NA\n", + "\\end{enumerate*}\n" ], "text/markdown": [ + "1. 'x_greater_1'\n", + "2. 'x_smaller_1'\n", + "3. 'x_smaller_0'\n", + "4. NA\n", "\n", - "A data.frame: 2 × 7\n", - "\n", - "| | X <int> | library.hashtag <chr> | m <chr> | measurement <chr> | delta_ef_value_group <chr> | delta_ef_value <dbl> | sample <chr> |\n", - "|---|---|---|---|---|---|---|---|\n", - "| 1 | 1 | 1.2 | M2 (1,15) | TP1 | x_greater_1 | 1.15 | 2.1 |\n", - "| 2 | 2 | 1.4 | M4 (3,1) | TP1 | x_greater_1 | 3.10 | 4.1 |\n", "\n" ], "text/plain": [ - " X library.hashtag m measurement delta_ef_value_group delta_ef_value\n", - "1 1 1.2 M2 (1,15) TP1 x_greater_1 1.15 \n", - "2 2 1.4 M4 (3,1) TP1 x_greater_1 3.10 \n", - " sample\n", - "1 2.1 \n", - "2 4.1 " + "[1] \"x_greater_1\" \"x_smaller_1\" \"x_smaller_0\" NA " ] }, "metadata": {}, @@ -2122,51 +1750,7 @@ } ], "source": [ - "head(ef_classification,2)" - ] - }, - { - "cell_type": "code", - "execution_count": 83, - "id": "1180f3c3-6a12-44ec-b32a-1a9af5e69748", - "metadata": {}, - "outputs": [ - { - "data": { - "text/html": [ - "\n", - "
  1. 'x_greater_1'
  2. 'x_smaller_1'
  3. 'x_smaller_0'
  4. NA
\n" - ], - "text/latex": [ - "\\begin{enumerate*}\n", - "\\item 'x\\_greater\\_1'\n", - "\\item 'x\\_smaller\\_1'\n", - "\\item 'x\\_smaller\\_0'\n", - "\\item NA\n", - "\\end{enumerate*}\n" - ], - "text/markdown": [ - "1. 'x_greater_1'\n", - "2. 'x_smaller_1'\n", - "3. 'x_smaller_0'\n", - "4. NA\n", - "\n", - "\n" - ], - "text/plain": [ - "[1] \"x_greater_1\" \"x_smaller_1\" \"x_smaller_0\" NA " - ] - }, - "metadata": {}, - "output_type": "display_data" - } - ], - "source": [ - "unique(ef_classification$delta_ef_value_group)" + "unique(ef_classification$delta_ef_value_group)" ] }, { @@ -2454,67 +2038,6 @@ "all_samples_info = merge(all_samples_info, ef_classification_data[,c('sample', 'delta_ef_value_class')], by.x = 'sample', by.y = 'sample', all.x = TRUE)" ] }, - { - "cell_type": "code", - "execution_count": 101, - "id": "06c4632a-92d9-4cdc-a73d-3a193387b69b", - "metadata": {}, - "outputs": [ - { - "data": { - "text/html": [ - "\n", - "\n", - "\n", - "\t\n", - "\t\n", - "\n", - "\n", - "\t\n", - "\t\n", - "\n", - "
A data.frame: 2 × 12
sampleidmeasurementsample_idsc_rna_seq_dataagesexclassificationgroupmeta_dataef_classification_datadelta_ef_value_class
<chr><chr><chr><chr><dbl><int><chr><chr><chr><dbl><dbl><chr>
1K1 1 TP0k1 055fvollstaendiger_ausschlussno_ccs1NANA
2K1010TP0k10157mccs ccs 1NANA
\n" - ], - "text/latex": [ - "A data.frame: 2 × 12\n", - "\\begin{tabular}{r|llllllllllll}\n", - " & sample & id & measurement & sample\\_id & sc\\_rna\\_seq\\_data & age & sex & classification & group & meta\\_data & ef\\_classification\\_data & delta\\_ef\\_value\\_class\\\\\n", - " & & & & & & & & & & & & \\\\\n", - "\\hline\n", - "\t1 & K1 & 1 & TP0 & k1 & 0 & 55 & f & vollstaendiger\\_ausschluss & no\\_ccs & 1 & NA & NA\\\\\n", - "\t2 & K10 & 10 & TP0 & k10 & 1 & 57 & m & ccs & ccs & 1 & NA & NA\\\\\n", - "\\end{tabular}\n" - ], - "text/markdown": [ - "\n", - "A data.frame: 2 × 12\n", - "\n", - "| | sample <chr> | id <chr> | measurement <chr> | sample_id <chr> | sc_rna_seq_data <dbl> | age <int> | sex <chr> | classification <chr> | group <chr> | meta_data <dbl> | ef_classification_data <dbl> | delta_ef_value_class <chr> |\n", - "|---|---|---|---|---|---|---|---|---|---|---|---|---|\n", - "| 1 | K1 | 1 | TP0 | k1 | 0 | 55 | f | vollstaendiger_ausschluss | no_ccs | 1 | NA | NA |\n", - "| 2 | K10 | 10 | TP0 | k10 | 1 | 57 | m | ccs | ccs | 1 | NA | NA |\n", - "\n" - ], - "text/plain": [ - " sample id measurement sample_id sc_rna_seq_data age sex\n", - "1 K1 1 TP0 k1 0 55 f \n", - "2 K10 10 TP0 k10 1 57 m \n", - " classification group meta_data ef_classification_data\n", - "1 vollstaendiger_ausschluss no_ccs 1 NA \n", - "2 ccs ccs 1 NA \n", - " delta_ef_value_class\n", - "1 NA \n", - "2 NA " - ] - }, - "metadata": {}, - "output_type": "display_data" - } - ], - "source": [ - "head(all_samples_info,2)" - ] - }, { "cell_type": "code", "execution_count": 102, @@ -2622,67 +2145,6 @@ "nrow(sample_data)" ] }, - { - "cell_type": "code", - "execution_count": 107, - "id": "570c488d-cdb8-4049-91fd-ec48889aaf13", - "metadata": {}, - "outputs": [ - { - "data": { - "text/html": [ - "\n", - "\n", - "\n", - "\t\n", - "\t\n", - "\n", - "\n", - "\t\n", - "\t\n", - "\n", - "
A data.frame: 2 × 20
sampleidmeasurementsample_idlibraryid.ynamereadpatternsequencefeature_typeXin_samplemeasurement_tpsc_rna_seq_dataagesexclassificationgroupmeta_data
<chr><chr><chr><chr><chr><chr><chr><chr><chr><chr><chr><lgl><int><chr><dbl><int><chr><chr><chr><dbl>
1K1 1 TP0k1 L13HTO_B0251No-CCS-1 R25PNNNNNNNNNN(BC)GTCAACTCTTTAGCGAntibody CaptureNA0No-CCS 155fvollstaendiger_ausschlussno_ccs1
2K1010TP0k10L11HTO_B0256Ch-CCS-10R25PNNNNNNNNNN(BC)GGTTGCCAGATGTCAAntibody CaptureNA1Chronic-CCS157mccs ccs 1
\n" - ], - "text/latex": [ - "A data.frame: 2 × 20\n", - "\\begin{tabular}{r|llllllllllllllllllll}\n", - " & sample & id & measurement & sample\\_id & library & id.y & name & read & pattern & sequence & feature\\_type & X & in\\_sample & measurement\\_tp & sc\\_rna\\_seq\\_data & age & sex & classification & group & meta\\_data\\\\\n", - " & & & & & & & & & & & & & & & & & & & & \\\\\n", - "\\hline\n", - "\t1 & K1 & 1 & TP0 & k1 & L13 & HTO\\_B0251 & No-CCS-1 & R2 & 5PNNNNNNNNNN(BC) & GTCAACTCTTTAGCG & Antibody Capture & NA & 0 & No-CCS & 1 & 55 & f & vollstaendiger\\_ausschluss & no\\_ccs & 1\\\\\n", - "\t2 & K10 & 10 & TP0 & k10 & L11 & HTO\\_B0256 & Ch-CCS-10 & R2 & 5PNNNNNNNNNN(BC) & GGTTGCCAGATGTCA & Antibody Capture & NA & 1 & Chronic-CCS & 1 & 57 & m & ccs & ccs & 1\\\\\n", - "\\end{tabular}\n" - ], - "text/markdown": [ - "\n", - "A data.frame: 2 × 20\n", - "\n", - "| | sample <chr> | id <chr> | measurement <chr> | sample_id <chr> | library <chr> | id.y <chr> | name <chr> | read <chr> | pattern <chr> | sequence <chr> | feature_type <chr> | X <lgl> | in_sample <int> | measurement_tp <chr> | sc_rna_seq_data <dbl> | age <int> | sex <chr> | classification <chr> | group <chr> | meta_data <dbl> |\n", - "|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|\n", - "| 1 | K1 | 1 | TP0 | k1 | L13 | HTO_B0251 | No-CCS-1 | R2 | 5PNNNNNNNNNN(BC) | GTCAACTCTTTAGCG | Antibody Capture | NA | 0 | No-CCS | 1 | 55 | f | vollstaendiger_ausschluss | no_ccs | 1 |\n", - "| 2 | K10 | 10 | TP0 | k10 | L11 | HTO_B0256 | Ch-CCS-10 | R2 | 5PNNNNNNNNNN(BC) | GGTTGCCAGATGTCA | Antibody Capture | NA | 1 | Chronic-CCS | 1 | 57 | m | ccs | ccs | 1 |\n", - "\n" - ], - "text/plain": [ - " sample id measurement sample_id library id.y name read\n", - "1 K1 1 TP0 k1 L13 HTO_B0251 No-CCS-1 R2 \n", - "2 K10 10 TP0 k10 L11 HTO_B0256 Ch-CCS-10 R2 \n", - " pattern sequence feature_type X in_sample measurement_tp\n", - "1 5PNNNNNNNNNN(BC) GTCAACTCTTTAGCG Antibody Capture NA 0 No-CCS \n", - "2 5PNNNNNNNNNN(BC) GGTTGCCAGATGTCA Antibody Capture NA 1 Chronic-CCS \n", - " sc_rna_seq_data age sex classification group meta_data\n", - "1 1 55 f vollstaendiger_ausschluss no_ccs 1 \n", - "2 1 57 m ccs ccs 1 " - ] - }, - "metadata": {}, - "output_type": "display_data" - } - ], - "source": [ - "head(sample_data,2)" - ] - }, { "cell_type": "code", "execution_count": 108, @@ -2722,72 +2184,6 @@ "nrow(sample_data)" ] }, - { - "cell_type": "code", - "execution_count": 110, - "id": "8baf7cf5-a7a1-4e0a-ac9e-927534634583", - "metadata": { - "tags": [] - }, - "outputs": [ - { - "data": { - "text/html": [ - "\n", - "\n", - "\n", - "\t\n", - "\t\n", - "\n", - "\n", - "\t\n", - "\t\n", - "\n", - "
A data.frame: 2 × 24
sampleidmeasurementsample_idlibraryid.ynamereadpatternsequence⋯sc_rna_seq_dataagesexclassificationgroupmeta_datadelta_ef_value_groupdelta_ef_valuedelta_ef_value_classef_classification_data
<chr><chr><chr><chr><chr><chr><chr><chr><chr><chr>⋯<dbl><int><chr><chr><chr><dbl><chr><dbl><chr><dbl>
1K1 1 TP0k1 L13HTO_B0251No-CCS-1 R25PNNNNNNNNNN(BC)GTCAACTCTTTAGCG⋯155fvollstaendiger_ausschlussno_ccs1NANANANA
2K1010TP0k10L11HTO_B0256Ch-CCS-10R25PNNNNNNNNNN(BC)GGTTGCCAGATGTCA⋯157mccs ccs 1NANANANA
\n" - ], - "text/latex": [ - "A data.frame: 2 × 24\n", - "\\begin{tabular}{r|lllllllllllllllllllll}\n", - " & sample & id & measurement & sample\\_id & library & id.y & name & read & pattern & sequence & ⋯ & sc\\_rna\\_seq\\_data & age & sex & classification & group & meta\\_data & delta\\_ef\\_value\\_group & delta\\_ef\\_value & delta\\_ef\\_value\\_class & ef\\_classification\\_data\\\\\n", - " & & & & & & & & & & & ⋯ & & & & & & & & & & \\\\\n", - "\\hline\n", - "\t1 & K1 & 1 & TP0 & k1 & L13 & HTO\\_B0251 & No-CCS-1 & R2 & 5PNNNNNNNNNN(BC) & GTCAACTCTTTAGCG & ⋯ & 1 & 55 & f & vollstaendiger\\_ausschluss & no\\_ccs & 1 & NA & NA & NA & NA\\\\\n", - "\t2 & K10 & 10 & TP0 & k10 & L11 & HTO\\_B0256 & Ch-CCS-10 & R2 & 5PNNNNNNNNNN(BC) & GGTTGCCAGATGTCA & ⋯ & 1 & 57 & m & ccs & ccs & 1 & NA & NA & NA & NA\\\\\n", - "\\end{tabular}\n" - ], - "text/markdown": [ - "\n", - "A data.frame: 2 × 24\n", - "\n", - "| | sample <chr> | id <chr> | measurement <chr> | sample_id <chr> | library <chr> | id.y <chr> | name <chr> | read <chr> | pattern <chr> | sequence <chr> | ⋯ ⋯ | sc_rna_seq_data <dbl> | age <int> | sex <chr> | classification <chr> | group <chr> | meta_data <dbl> | delta_ef_value_group <chr> | delta_ef_value <dbl> | delta_ef_value_class <chr> | ef_classification_data <dbl> |\n", - "|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|\n", - "| 1 | K1 | 1 | TP0 | k1 | L13 | HTO_B0251 | No-CCS-1 | R2 | 5PNNNNNNNNNN(BC) | GTCAACTCTTTAGCG | ⋯ | 1 | 55 | f | vollstaendiger_ausschluss | no_ccs | 1 | NA | NA | NA | NA |\n", - "| 2 | K10 | 10 | TP0 | k10 | L11 | HTO_B0256 | Ch-CCS-10 | R2 | 5PNNNNNNNNNN(BC) | GGTTGCCAGATGTCA | ⋯ | 1 | 57 | m | ccs | ccs | 1 | NA | NA | NA | NA |\n", - "\n" - ], - "text/plain": [ - " sample id measurement sample_id library id.y name read\n", - "1 K1 1 TP0 k1 L13 HTO_B0251 No-CCS-1 R2 \n", - "2 K10 10 TP0 k10 L11 HTO_B0256 Ch-CCS-10 R2 \n", - " pattern sequence ⋯ sc_rna_seq_data age sex\n", - "1 5PNNNNNNNNNN(BC) GTCAACTCTTTAGCG ⋯ 1 55 f \n", - "2 5PNNNNNNNNNN(BC) GGTTGCCAGATGTCA ⋯ 1 57 m \n", - " classification group meta_data delta_ef_value_group\n", - "1 vollstaendiger_ausschluss no_ccs 1 NA \n", - "2 ccs ccs 1 NA \n", - " delta_ef_value delta_ef_value_class ef_classification_data\n", - "1 NA NA NA \n", - "2 NA NA NA " - ] - }, - "metadata": {}, - "output_type": "display_data" - } - ], - "source": [ - "head(sample_data,2)" - ] - }, { "cell_type": "code", "execution_count": 111, @@ -2893,374 +2289,6 @@ "print(file.info(path)$mtime)" ] }, - { - "cell_type": "code", - "execution_count": 116, - "id": "12eedde4-8726-49a0-b46c-c4b8df40858c", - "metadata": { - "tags": [] - }, - "outputs": [ - { - "data": { - "text/html": [ - "\n", - "\n", - "\n", - "\t\n", - "\t\n", - "\n", - "\n", - "\t\n", - "\t\n", - "\n", - "
A data.frame: 2 × 4
CKCK_MBTroponinsample_id
<int><chr><dbl><chr>
11280.169m2.1
2 NA NAm3.1
\n" - ], - "text/latex": [ - "A data.frame: 2 × 4\n", - "\\begin{tabular}{r|llll}\n", - " & CK & CK\\_MB & Troponin & sample\\_id\\\\\n", - " & & & & \\\\\n", - "\\hline\n", - "\t1 & 128 & & 0.169 & m2.1\\\\\n", - "\t2 & NA & & NA & m3.1\\\\\n", - "\\end{tabular}\n" - ], - "text/markdown": [ - "\n", - "A data.frame: 2 × 4\n", - "\n", - "| | CK <int> | CK_MB <chr> | Troponin <dbl> | sample_id <chr> |\n", - "|---|---|---|---|---|\n", - "| 1 | 128 | | 0.169 | m2.1 |\n", - "| 2 | NA | | NA | m3.1 |\n", - "\n" - ], - "text/plain": [ - " CK CK_MB Troponin sample_id\n", - "1 128 0.169 m2.1 \n", - "2 NA NA m3.1 " - ] - }, - "metadata": {}, - "output_type": "display_data" - } - ], - "source": [ - "head(clinical,2)" - ] - }, - { - "cell_type": "code", - "execution_count": 117, - "id": "4fc6b00b-fa39-4885-9ee9-9eb1dcbc8a37", - "metadata": {}, - "outputs": [ - { - "data": { - "text/html": [ - "\n", - "\n", - "\n", - "\t\n", - "\t\n", - "\n", - "\n", - "\t\n", - "\t\n", - "\n", - "
A data.frame: 2 × 2
sample_idCRP
<chr><chr>
1k20.1
2k40.3
\n" - ], - "text/latex": [ - "A data.frame: 2 × 2\n", - "\\begin{tabular}{r|ll}\n", - " & sample\\_id & CRP\\\\\n", - " & & \\\\\n", - "\\hline\n", - "\t1 & k2 & 0.1\\\\\n", - "\t2 & k4 & 0.3\\\\\n", - "\\end{tabular}\n" - ], - "text/markdown": [ - "\n", - "A data.frame: 2 × 2\n", - "\n", - "| | sample_id <chr> | CRP <chr> |\n", - "|---|---|---|\n", - "| 1 | k2 | 0.1 |\n", - "| 2 | k4 | 0.3 |\n", - "\n" - ], - "text/plain": [ - " sample_id CRP\n", - "1 k2 0.1\n", - "2 k4 0.3" - ] - }, - "metadata": {}, - "output_type": "display_data" - } - ], - "source": [ - "head(clinical_crp,2)" - ] - }, - { - "cell_type": "code", - "execution_count": 118, - "id": "b188beb4-5353-40e4-976c-092c99c432ca", - "metadata": {}, - "outputs": [ - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Warning message in unique(as.numeric(clinical_crp$CRP)):\n", - "“NAs introduced by coercion”\n" - ] - }, - { - "data": { - "text/html": [ - "\n", - "
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A data.frame: 2 × 5
sample_idCKCK_MBTroponinCRP
<chr><int><chr><dbl><chr>
1k1 430.0130.4
2k10NA NA0.2
\n" - ], - "text/latex": [ - "A data.frame: 2 × 5\n", - "\\begin{tabular}{r|lllll}\n", - " & sample\\_id & CK & CK\\_MB & Troponin & CRP\\\\\n", - " & & & & & \\\\\n", - "\\hline\n", - "\t1 & k1 & 43 & & 0.013 & 0.4\\\\\n", - "\t2 & k10 & NA & & NA & 0.2\\\\\n", - "\\end{tabular}\n" - ], - "text/markdown": [ - "\n", - "A data.frame: 2 × 5\n", - "\n", - "| | sample_id <chr> | CK <int> | CK_MB <chr> | Troponin <dbl> | CRP <chr> |\n", - "|---|---|---|---|---|---|\n", - "| 1 | k1 | 43 | | 0.013 | 0.4 |\n", - "| 2 | k10 | NA | | NA | 0.2 |\n", - "\n" - ], - "text/plain": [ - " sample_id CK CK_MB Troponin CRP\n", - "1 k1 43 0.013 0.4\n", - "2 k10 NA NA 0.2" - ] - }, - "metadata": {}, - "output_type": "display_data" - } - ], - "source": [ - "head(clinical,2)" - ] - }, { "cell_type": "code", "execution_count": 128, @@ -3584,79 +2557,15 @@ "source": [ "nrow(all_samples_info)" ] - }, - { - "cell_type": "code", - "execution_count": 136, - "id": "542b84d0-a474-420e-94c9-e356d0633cec", - "metadata": {}, - "outputs": [], - "source": [ - "all_samples_info = merge(all_samples_info, clinical[,c('sample_id', 'clinical_data', 'complete_clinical_data', 'min_1_clinical_value')], by.x = 'sample_id', by.y = 'sample_id')" - ] - }, - { - "cell_type": "code", - "execution_count": 137, - "id": "91d71ba0-689b-4fc0-bbf0-8eaf5d63e829", - "metadata": {}, - "outputs": [ - { - "data": { - "text/html": [ - "\n", - "\n", - "\n", - "\t\n", - "\t\n", - "\n", - "\n", - "\t\n", - "\t\n", - "\n", - "
A data.frame: 2 × 15
sample_idsampleidmeasurementsc_rna_seq_dataagesexclassificationgroupmeta_dataef_classification_datadelta_ef_value_classclinical_datacomplete_clinical_datamin_1_clinical_value
<chr><chr><chr><chr><dbl><int><chr><chr><chr><dbl><dbl><chr><dbl><dbl><dbl>
1k1 K1 1 TP0055fvollstaendiger_ausschlussno_ccs10NA101
2k10K1010TP0157mccs ccs 10NA101
\n" - ], - "text/latex": [ - "A data.frame: 2 × 15\n", - "\\begin{tabular}{r|lllllllllllllll}\n", - " & sample\\_id & sample & id & measurement & sc\\_rna\\_seq\\_data & age & sex & classification & group & meta\\_data & ef\\_classification\\_data & delta\\_ef\\_value\\_class & clinical\\_data & complete\\_clinical\\_data & min\\_1\\_clinical\\_value\\\\\n", - " & & & & & & & & & & & & & & & \\\\\n", - "\\hline\n", - "\t1 & k1 & K1 & 1 & TP0 & 0 & 55 & f & vollstaendiger\\_ausschluss & no\\_ccs & 1 & 0 & NA & 1 & 0 & 1\\\\\n", - "\t2 & k10 & K10 & 10 & TP0 & 1 & 57 & m & ccs & ccs & 1 & 0 & NA & 1 & 0 & 1\\\\\n", - "\\end{tabular}\n" - ], - "text/markdown": [ - "\n", - "A data.frame: 2 × 15\n", - "\n", - "| | sample_id <chr> | sample <chr> | id <chr> | measurement <chr> | sc_rna_seq_data <dbl> | age <int> | sex <chr> | classification <chr> | group <chr> | meta_data <dbl> | ef_classification_data <dbl> | delta_ef_value_class <chr> | clinical_data <dbl> | complete_clinical_data <dbl> | min_1_clinical_value <dbl> |\n", - "|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|\n", - "| 1 | k1 | K1 | 1 | TP0 | 0 | 55 | f | vollstaendiger_ausschluss | no_ccs | 1 | 0 | NA | 1 | 0 | 1 |\n", - "| 2 | k10 | K10 | 10 | TP0 | 1 | 57 | m | ccs | ccs | 1 | 0 | NA | 1 | 0 | 1 |\n", - "\n" - ], - "text/plain": [ - " sample_id sample id measurement sc_rna_seq_data age sex\n", - "1 k1 K1 1 TP0 0 55 f \n", - "2 k10 K10 10 TP0 1 57 m \n", - " classification group meta_data ef_classification_data\n", - "1 vollstaendiger_ausschluss no_ccs 1 0 \n", - "2 ccs ccs 1 0 \n", - " delta_ef_value_class clinical_data complete_clinical_data\n", - "1 NA 1 0 \n", - "2 NA 1 0 \n", - " min_1_clinical_value\n", - "1 1 \n", - "2 1 " - ] - }, - "metadata": {}, - "output_type": "display_data" - } - ], + }, + { + "cell_type": "code", + "execution_count": 136, + "id": "542b84d0-a474-420e-94c9-e356d0633cec", + "metadata": {}, + "outputs": [], "source": [ - "head(all_samples_info,2)" + "all_samples_info = merge(all_samples_info, clinical[,c('sample_id', 'clinical_data', 'complete_clinical_data', 'min_1_clinical_value')], by.x = 'sample_id', by.y = 'sample_id')" ] }, { @@ -3756,70 +2665,6 @@ "nrow(sample_data)" ] }, - { - "cell_type": "code", - "execution_count": 142, - "id": "85dc0cd0-a3c8-426b-91fb-b300d4c5ba9e", - "metadata": {}, - "outputs": [ - { - "data": { - "text/html": [ - "\n", - "\n", - "\n", - "\t\n", - "\t\n", - "\n", - "\n", - "\t\n", - "\t\n", - "\n", - "
A data.frame: 2 × 24
sampleidmeasurementsample_idlibraryid.ynamereadpatternsequence⋯sc_rna_seq_dataagesexclassificationgroupmeta_datadelta_ef_value_groupdelta_ef_valuedelta_ef_value_classef_classification_data
<chr><chr><chr><chr><chr><chr><chr><chr><chr><chr>⋯<dbl><int><chr><chr><chr><dbl><chr><dbl><chr><dbl>
1K1 1 TP0k1 L13HTO_B0251No-CCS-1 R25PNNNNNNNNNN(BC)GTCAACTCTTTAGCG⋯155fvollstaendiger_ausschlussno_ccs1NANANA0
2K1010TP0k10L11HTO_B0256Ch-CCS-10R25PNNNNNNNNNN(BC)GGTTGCCAGATGTCA⋯157mccs ccs 1NANANA0
\n" - ], - "text/latex": [ - "A data.frame: 2 × 24\n", - "\\begin{tabular}{r|lllllllllllllllllllll}\n", - " & sample & id & measurement & sample\\_id & library & id.y & name & read & pattern & sequence & ⋯ & sc\\_rna\\_seq\\_data & age & sex & classification & group & meta\\_data & delta\\_ef\\_value\\_group & delta\\_ef\\_value & delta\\_ef\\_value\\_class & ef\\_classification\\_data\\\\\n", - " & & & & & & & & & & & ⋯ & & & & & & & & & & \\\\\n", - "\\hline\n", - "\t1 & K1 & 1 & TP0 & k1 & L13 & HTO\\_B0251 & No-CCS-1 & R2 & 5PNNNNNNNNNN(BC) & GTCAACTCTTTAGCG & ⋯ & 1 & 55 & f & vollstaendiger\\_ausschluss & no\\_ccs & 1 & NA & NA & NA & 0\\\\\n", - "\t2 & K10 & 10 & TP0 & k10 & L11 & HTO\\_B0256 & Ch-CCS-10 & R2 & 5PNNNNNNNNNN(BC) & GGTTGCCAGATGTCA & ⋯ & 1 & 57 & m & ccs & ccs & 1 & NA & NA & NA & 0\\\\\n", - "\\end{tabular}\n" - ], - "text/markdown": [ - "\n", - "A data.frame: 2 × 24\n", - "\n", - "| | sample <chr> | id <chr> | measurement <chr> | sample_id <chr> | library <chr> | id.y <chr> | name <chr> | read <chr> | pattern <chr> | sequence <chr> | ⋯ ⋯ | sc_rna_seq_data <dbl> | age <int> | sex <chr> | classification <chr> | group <chr> | meta_data <dbl> | delta_ef_value_group <chr> | delta_ef_value <dbl> | delta_ef_value_class <chr> | ef_classification_data <dbl> |\n", - "|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|\n", - "| 1 | K1 | 1 | TP0 | k1 | L13 | HTO_B0251 | No-CCS-1 | R2 | 5PNNNNNNNNNN(BC) | GTCAACTCTTTAGCG | ⋯ | 1 | 55 | f | vollstaendiger_ausschluss | no_ccs | 1 | NA | NA | NA | 0 |\n", - "| 2 | K10 | 10 | TP0 | k10 | L11 | HTO_B0256 | Ch-CCS-10 | R2 | 5PNNNNNNNNNN(BC) | GGTTGCCAGATGTCA | ⋯ | 1 | 57 | m | ccs | ccs | 1 | NA | NA | NA | 0 |\n", - "\n" - ], - "text/plain": [ - " sample id measurement sample_id library id.y name read\n", - "1 K1 1 TP0 k1 L13 HTO_B0251 No-CCS-1 R2 \n", - "2 K10 10 TP0 k10 L11 HTO_B0256 Ch-CCS-10 R2 \n", - " pattern sequence ⋯ sc_rna_seq_data age sex\n", - "1 5PNNNNNNNNNN(BC) GTCAACTCTTTAGCG ⋯ 1 55 f \n", - "2 5PNNNNNNNNNN(BC) GGTTGCCAGATGTCA ⋯ 1 57 m \n", - " classification group meta_data delta_ef_value_group\n", - "1 vollstaendiger_ausschluss no_ccs 1 NA \n", - "2 ccs ccs 1 NA \n", - " delta_ef_value delta_ef_value_class ef_classification_data\n", - "1 NA NA 0 \n", - "2 NA NA 0 " - ] - }, - "metadata": {}, - "output_type": "display_data" - } - ], - "source": [ - "head(sample_data,2)" - ] - }, { "cell_type": "code", "execution_count": 143, @@ -3859,72 +2704,6 @@ "nrow(sample_data)" ] }, - { - "cell_type": "code", - "execution_count": 145, - "id": "41278fbc-209f-426f-ad7d-d9d3b3fbf2e4", - "metadata": { - "tags": [] - }, - "outputs": [ - { - "data": { - "text/html": [ - "\n", - "\n", - "\n", - "\t\n", - "\t\n", - "\n", - "\n", - "\t\n", - "\t\n", - "\n", - "
A data.frame: 2 × 31
sample_idsampleidmeasurementlibraryid.ynamereadpatternsequence⋯delta_ef_valuedelta_ef_value_classef_classification_dataCKCK_MBTroponinCRPclinical_datacomplete_clinical_datamin_1_clinical_value
<chr><chr><chr><chr><chr><chr><chr><chr><chr><chr>⋯<dbl><chr><dbl><int><chr><dbl><chr><dbl><dbl><dbl>
1k1 K1 1 TP0L13HTO_B0251No-CCS-1 R25PNNNNNNNNNN(BC)GTCAACTCTTTAGCG⋯NANA0430.0130.4101
2k10K1010TP0L11HTO_B0256Ch-CCS-10R25PNNNNNNNNNN(BC)GGTTGCCAGATGTCA⋯NANA0NA NA0.2101
\n" - ], - "text/latex": [ - "A data.frame: 2 × 31\n", - "\\begin{tabular}{r|lllllllllllllllllllll}\n", - " & sample\\_id & sample & id & measurement & library & id.y & name & read & pattern & sequence & ⋯ & delta\\_ef\\_value & delta\\_ef\\_value\\_class & ef\\_classification\\_data & CK & CK\\_MB & Troponin & CRP & clinical\\_data & complete\\_clinical\\_data & min\\_1\\_clinical\\_value\\\\\n", - " & & & & & & & & & & & ⋯ & & & & & & & & & & \\\\\n", - "\\hline\n", - "\t1 & k1 & K1 & 1 & TP0 & L13 & HTO\\_B0251 & No-CCS-1 & R2 & 5PNNNNNNNNNN(BC) & GTCAACTCTTTAGCG & ⋯ & NA & NA & 0 & 43 & & 0.013 & 0.4 & 1 & 0 & 1\\\\\n", - "\t2 & k10 & K10 & 10 & TP0 & L11 & HTO\\_B0256 & Ch-CCS-10 & R2 & 5PNNNNNNNNNN(BC) & GGTTGCCAGATGTCA & ⋯ & NA & NA & 0 & NA & & NA & 0.2 & 1 & 0 & 1\\\\\n", - "\\end{tabular}\n" - ], - "text/markdown": [ - "\n", - "A data.frame: 2 × 31\n", - "\n", - "| | sample_id <chr> | sample <chr> | id <chr> | measurement <chr> | library <chr> | id.y <chr> | name <chr> | read <chr> | pattern <chr> | sequence <chr> | ⋯ ⋯ | delta_ef_value <dbl> | delta_ef_value_class <chr> | ef_classification_data <dbl> | CK <int> | CK_MB <chr> | Troponin <dbl> | CRP <chr> | clinical_data <dbl> | complete_clinical_data <dbl> | min_1_clinical_value <dbl> |\n", - "|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|\n", - "| 1 | k1 | K1 | 1 | TP0 | L13 | HTO_B0251 | No-CCS-1 | R2 | 5PNNNNNNNNNN(BC) | GTCAACTCTTTAGCG | ⋯ | NA | NA | 0 | 43 | | 0.013 | 0.4 | 1 | 0 | 1 |\n", - "| 2 | k10 | K10 | 10 | TP0 | L11 | HTO_B0256 | Ch-CCS-10 | R2 | 5PNNNNNNNNNN(BC) | GGTTGCCAGATGTCA | ⋯ | NA | NA | 0 | NA | | NA | 0.2 | 1 | 0 | 1 |\n", - "\n" - ], - "text/plain": [ - " sample_id sample id measurement library id.y name read\n", - "1 k1 K1 1 TP0 L13 HTO_B0251 No-CCS-1 R2 \n", - "2 k10 K10 10 TP0 L11 HTO_B0256 Ch-CCS-10 R2 \n", - " pattern sequence ⋯ delta_ef_value delta_ef_value_class\n", - "1 5PNNNNNNNNNN(BC) GTCAACTCTTTAGCG ⋯ NA NA \n", - "2 5PNNNNNNNNNN(BC) GGTTGCCAGATGTCA ⋯ NA NA \n", - " ef_classification_data CK CK_MB Troponin CRP clinical_data\n", - "1 0 43 0.013 0.4 1 \n", - "2 0 NA NA 0.2 1 \n", - " complete_clinical_data min_1_clinical_value\n", - "1 0 1 \n", - "2 0 1 " - ] - }, - "metadata": {}, - "output_type": "display_data" - } - ], - "source": [ - "head(sample_data,2)" - ] - }, { "cell_type": "code", "execution_count": 146, @@ -4259,70 +3038,6 @@ "### Add information about available cytokine data" ] }, - { - "cell_type": "code", - "execution_count": 159, - "id": "63398678-189f-42b2-bea9-7347212b415b", - "metadata": {}, - "outputs": [ - { - "data": { - "text/html": [ - "\n", - "\n", - "\n", - "\t\n", - "\t\n", - "\n", - "\n", - "\t\n", - "\t\n", - "\n", - "
A data.frame: 2 × 15
sample_idsampleidmeasurementsc_rna_seq_dataagesexclassificationgroupmeta_dataef_classification_datadelta_ef_value_classclinical_datacomplete_clinical_datamin_1_clinical_value
<chr><chr><chr><chr><dbl><int><chr><chr><chr><dbl><dbl><chr><dbl><dbl><dbl>
1k1 K1 1 TP0055fvollstaendiger_ausschlussno_ccs10NA101
2k10K1010TP0157mccs ccs 10NA101
\n" - ], - "text/latex": [ - "A data.frame: 2 × 15\n", - "\\begin{tabular}{r|lllllllllllllll}\n", - " & sample\\_id & sample & id & measurement & sc\\_rna\\_seq\\_data & age & sex & classification & group & meta\\_data & ef\\_classification\\_data & delta\\_ef\\_value\\_class & clinical\\_data & complete\\_clinical\\_data & min\\_1\\_clinical\\_value\\\\\n", - " & & & & & & & & & & & & & & & \\\\\n", - "\\hline\n", - "\t1 & k1 & K1 & 1 & TP0 & 0 & 55 & f & vollstaendiger\\_ausschluss & no\\_ccs & 1 & 0 & NA & 1 & 0 & 1\\\\\n", - "\t2 & k10 & K10 & 10 & TP0 & 1 & 57 & m & ccs & ccs & 1 & 0 & NA & 1 & 0 & 1\\\\\n", - "\\end{tabular}\n" - ], - "text/markdown": [ - "\n", - "A data.frame: 2 × 15\n", - "\n", - "| | sample_id <chr> | sample <chr> | id <chr> | measurement <chr> | sc_rna_seq_data <dbl> | age <int> | sex <chr> | classification <chr> | group <chr> | meta_data <dbl> | ef_classification_data <dbl> | delta_ef_value_class <chr> | clinical_data <dbl> | complete_clinical_data <dbl> | min_1_clinical_value <dbl> |\n", - "|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|\n", - "| 1 | k1 | K1 | 1 | TP0 | 0 | 55 | f | vollstaendiger_ausschluss | no_ccs | 1 | 0 | NA | 1 | 0 | 1 |\n", - "| 2 | k10 | K10 | 10 | TP0 | 1 | 57 | m | ccs | ccs | 1 | 0 | NA | 1 | 0 | 1 |\n", - "\n" - ], - "text/plain": [ - " sample_id sample id measurement sc_rna_seq_data age sex\n", - "1 k1 K1 1 TP0 0 55 f \n", - "2 k10 K10 10 TP0 1 57 m \n", - " classification group meta_data ef_classification_data\n", - "1 vollstaendiger_ausschluss no_ccs 1 0 \n", - "2 ccs ccs 1 0 \n", - " delta_ef_value_class clinical_data complete_clinical_data\n", - "1 NA 1 0 \n", - "2 NA 1 0 \n", - " min_1_clinical_value\n", - "1 1 \n", - "2 1 " - ] - }, - "metadata": {}, - "output_type": "display_data" - } - ], - "source": [ - "head(all_samples_info,2)" - ] - }, { "cell_type": "code", "execution_count": 160, @@ -4395,70 +3110,6 @@ "nrow(all_samples_info)" ] }, - { - "cell_type": "code", - "execution_count": 164, - "id": "188fbff7-4621-41b6-a743-c609725dffed", - "metadata": {}, - "outputs": [ - { - "data": { - "text/html": [ - "\n", - "\n", - "\n", - "\t\n", - "\t\n", - "\n", - "\n", - "\t\n", - "\t\n", - "\n", - "
A data.frame: 2 × 16
sample_idsampleidmeasurementsc_rna_seq_dataagesexclassificationgroupmeta_dataef_classification_datadelta_ef_value_classclinical_datacomplete_clinical_datamin_1_clinical_valuecytokine_data
<chr><chr><chr><chr><dbl><int><chr><chr><chr><dbl><dbl><chr><dbl><dbl><dbl><dbl>
1k1 K1 1 TP0055fvollstaendiger_ausschlussno_ccs10NA1011
2k10K1010TP0157mccs ccs 10NA1011
\n" - ], - "text/latex": [ - "A data.frame: 2 × 16\n", - "\\begin{tabular}{r|llllllllllllllll}\n", - " & sample\\_id & sample & id & measurement & sc\\_rna\\_seq\\_data & age & sex & classification & group & meta\\_data & ef\\_classification\\_data & delta\\_ef\\_value\\_class & clinical\\_data & complete\\_clinical\\_data & min\\_1\\_clinical\\_value & cytokine\\_data\\\\\n", - " & & & & & & & & & & & & & & & & \\\\\n", - "\\hline\n", - "\t1 & k1 & K1 & 1 & TP0 & 0 & 55 & f & vollstaendiger\\_ausschluss & no\\_ccs & 1 & 0 & NA & 1 & 0 & 1 & 1\\\\\n", - "\t2 & k10 & K10 & 10 & TP0 & 1 & 57 & m & ccs & ccs & 1 & 0 & NA & 1 & 0 & 1 & 1\\\\\n", - "\\end{tabular}\n" - ], - "text/markdown": [ - "\n", - "A data.frame: 2 × 16\n", - "\n", - "| | sample_id <chr> | sample <chr> | id <chr> | measurement <chr> | sc_rna_seq_data <dbl> | age <int> | sex <chr> | classification <chr> | group <chr> | meta_data <dbl> | ef_classification_data <dbl> | delta_ef_value_class <chr> | clinical_data <dbl> | complete_clinical_data <dbl> | min_1_clinical_value <dbl> | cytokine_data <dbl> |\n", - "|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|\n", - "| 1 | k1 | K1 | 1 | TP0 | 0 | 55 | f | vollstaendiger_ausschluss | no_ccs | 1 | 0 | NA | 1 | 0 | 1 | 1 |\n", - "| 2 | k10 | K10 | 10 | TP0 | 1 | 57 | m | ccs | ccs | 1 | 0 | NA | 1 | 0 | 1 | 1 |\n", - "\n" - ], - "text/plain": [ - " sample_id sample id measurement sc_rna_seq_data age sex\n", - "1 k1 K1 1 TP0 0 55 f \n", - "2 k10 K10 10 TP0 1 57 m \n", - " classification group meta_data ef_classification_data\n", - "1 vollstaendiger_ausschluss no_ccs 1 0 \n", - "2 ccs ccs 1 0 \n", - " delta_ef_value_class clinical_data complete_clinical_data\n", - "1 NA 1 0 \n", - "2 NA 1 0 \n", - " min_1_clinical_value cytokine_data\n", - "1 1 1 \n", - "2 1 1 " - ] - }, - "metadata": {}, - "output_type": "display_data" - } - ], - "source": [ - "head(all_samples_info,2)" - ] - }, { "cell_type": "code", "execution_count": 165, @@ -5582,16 +4233,6 @@ "check_similarity3[check_similarity3$sample_id == 'k4',]" ] }, - { - "cell_type": "code", - "execution_count": 198, - "id": "5774f067-6d55-467a-8cf2-4375a21f3fbb", - "metadata": {}, - "outputs": [], - "source": [ - "### Not sure with which file to continue? - To discuss with Victoria" - ] - }, { "cell_type": "code", "execution_count": 199, @@ -5661,70 +4302,6 @@ "### Investigate sample IDs + compare with remaining data" ] }, - { - "cell_type": "code", - "execution_count": 204, - "id": "c78ab9ea-7a4c-44f9-aeb9-62466add3ab9", - "metadata": {}, - "outputs": [ - { - "data": { - "text/html": [ - "\n", - "\n", - "\n", - "\t\n", - "\t\n", - "\n", - "\n", - "\t\n", - "\t\n", - "\n", - "
A data.frame: 2 × 16
sample_idsampleidmeasurementsc_rna_seq_dataagesexclassificationgroupmeta_dataef_classification_datadelta_ef_value_classclinical_datacomplete_clinical_datamin_1_clinical_valuecytokine_data
<chr><chr><chr><chr><dbl><int><chr><chr><chr><dbl><dbl><chr><dbl><dbl><dbl><dbl>
1k1 K1 1 TP0055fvollstaendiger_ausschlussno_ccs10NA1011
2k10K1010TP0157mccs ccs 10NA1011
\n" - ], - "text/latex": [ - "A data.frame: 2 × 16\n", - "\\begin{tabular}{r|llllllllllllllll}\n", - " & sample\\_id & sample & id & measurement & sc\\_rna\\_seq\\_data & age & sex & classification & group & meta\\_data & ef\\_classification\\_data & delta\\_ef\\_value\\_class & clinical\\_data & complete\\_clinical\\_data & min\\_1\\_clinical\\_value & cytokine\\_data\\\\\n", - " & & & & & & & & & & & & & & & & \\\\\n", - "\\hline\n", - "\t1 & k1 & K1 & 1 & TP0 & 0 & 55 & f & vollstaendiger\\_ausschluss & no\\_ccs & 1 & 0 & NA & 1 & 0 & 1 & 1\\\\\n", - "\t2 & k10 & K10 & 10 & TP0 & 1 & 57 & m & ccs & ccs & 1 & 0 & NA & 1 & 0 & 1 & 1\\\\\n", - "\\end{tabular}\n" - ], - "text/markdown": [ - "\n", - "A data.frame: 2 × 16\n", - "\n", - "| | sample_id <chr> | sample <chr> | id <chr> | measurement <chr> | sc_rna_seq_data <dbl> | age <int> | sex <chr> | classification <chr> | group <chr> | meta_data <dbl> | ef_classification_data <dbl> | delta_ef_value_class <chr> | clinical_data <dbl> | complete_clinical_data <dbl> | min_1_clinical_value <dbl> | cytokine_data <dbl> |\n", - "|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|\n", - "| 1 | k1 | K1 | 1 | TP0 | 0 | 55 | f | vollstaendiger_ausschluss | no_ccs | 1 | 0 | NA | 1 | 0 | 1 | 1 |\n", - "| 2 | k10 | K10 | 10 | TP0 | 1 | 57 | m | ccs | ccs | 1 | 0 | NA | 1 | 0 | 1 | 1 |\n", - "\n" - ], - "text/plain": [ - " sample_id sample id measurement sc_rna_seq_data age sex\n", - "1 k1 K1 1 TP0 0 55 f \n", - "2 k10 K10 10 TP0 1 57 m \n", - " classification group meta_data ef_classification_data\n", - "1 vollstaendiger_ausschluss no_ccs 1 0 \n", - "2 ccs ccs 1 0 \n", - " delta_ef_value_class clinical_data complete_clinical_data\n", - "1 NA 1 0 \n", - "2 NA 1 0 \n", - " min_1_clinical_value cytokine_data\n", - "1 1 1 \n", - "2 1 1 " - ] - }, - "metadata": {}, - "output_type": "display_data" - } - ], - "source": [ - "head(all_samples_info,2)" - ] - }, { "cell_type": "code", "execution_count": 205, @@ -5764,70 +4341,6 @@ "nrow(all_samples_info)" ] }, - { - "cell_type": "code", - "execution_count": 207, - "id": "70eec507-b66e-4bea-bde7-2ea57a2db845", - "metadata": {}, - "outputs": [ - { - "data": { - "text/html": [ - "\n", - "\n", - "\n", - "\t\n", - "\t\n", - "\n", - "\n", - "\t\n", - "\t\n", - "\n", - "
A data.frame: 2 × 17
sample_idsampleidmeasurementsc_rna_seq_dataagesexclassificationgroupmeta_dataef_classification_datadelta_ef_value_classclinical_datacomplete_clinical_datamin_1_clinical_valuecytokine_dataneutrophil_data
<chr><chr><chr><chr><dbl><int><chr><chr><chr><dbl><dbl><chr><dbl><dbl><dbl><dbl><dbl>
1k1 K1 1 TP0055fvollstaendiger_ausschlussno_ccs10NA10111
2k10K1010TP0157mccs ccs 10NA10111
\n" - ], - "text/latex": [ - "A data.frame: 2 × 17\n", - "\\begin{tabular}{r|lllllllllllllllll}\n", - " & sample\\_id & sample & id & measurement & sc\\_rna\\_seq\\_data & age & sex & classification & group & meta\\_data & ef\\_classification\\_data & delta\\_ef\\_value\\_class & clinical\\_data & complete\\_clinical\\_data & min\\_1\\_clinical\\_value & cytokine\\_data & neutrophil\\_data\\\\\n", - " & & & & & & & & & & & & & & & & & \\\\\n", - "\\hline\n", - "\t1 & k1 & K1 & 1 & TP0 & 0 & 55 & f & vollstaendiger\\_ausschluss & no\\_ccs & 1 & 0 & NA & 1 & 0 & 1 & 1 & 1\\\\\n", - "\t2 & k10 & K10 & 10 & TP0 & 1 & 57 & m & ccs & ccs & 1 & 0 & NA & 1 & 0 & 1 & 1 & 1\\\\\n", - "\\end{tabular}\n" - ], - "text/markdown": [ - "\n", - "A data.frame: 2 × 17\n", - "\n", - "| | sample_id <chr> | sample <chr> | id <chr> | measurement <chr> | sc_rna_seq_data <dbl> | age <int> | sex <chr> | classification <chr> | group <chr> | meta_data <dbl> | ef_classification_data <dbl> | delta_ef_value_class <chr> | clinical_data <dbl> | complete_clinical_data <dbl> | min_1_clinical_value <dbl> | cytokine_data <dbl> | neutrophil_data <dbl> |\n", - "|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|\n", - "| 1 | k1 | K1 | 1 | TP0 | 0 | 55 | f | vollstaendiger_ausschluss | no_ccs | 1 | 0 | NA | 1 | 0 | 1 | 1 | 1 |\n", - "| 2 | k10 | K10 | 10 | TP0 | 1 | 57 | m | ccs | ccs | 1 | 0 | NA | 1 | 0 | 1 | 1 | 1 |\n", - "\n" - ], - "text/plain": [ - " sample_id sample id measurement sc_rna_seq_data age sex\n", - "1 k1 K1 1 TP0 0 55 f \n", - "2 k10 K10 10 TP0 1 57 m \n", - " classification group meta_data ef_classification_data\n", - "1 vollstaendiger_ausschluss no_ccs 1 0 \n", - "2 ccs ccs 1 0 \n", - " delta_ef_value_class clinical_data complete_clinical_data\n", - "1 NA 1 0 \n", - "2 NA 1 0 \n", - " min_1_clinical_value cytokine_data neutrophil_data\n", - "1 1 1 1 \n", - "2 1 1 1 " - ] - }, - "metadata": {}, - "output_type": "display_data" - } - ], - "source": [ - "head(all_samples_info,2)" - ] - }, { "cell_type": "code", "execution_count": 208, @@ -6550,77 +5063,13 @@ "146" ], "text/latex": [ - "146" - ], - "text/markdown": [ - "146" - ], - "text/plain": [ - "[1] 146" - ] - }, - "metadata": {}, - "output_type": "display_data" - } - ], - "source": [ - "nrow(all_samples_info)" - ] - }, - { - "cell_type": "code", - "execution_count": 238, - "id": "2ed9c8e1-032d-4e71-a14d-2f27fc92a131", - "metadata": {}, - "outputs": [ - { - "data": { - "text/html": [ - "\n", - "\n", - "\n", - "\t\n", - "\t\n", - "\n", - "\n", - "\t\n", - "\t\n", - "\n", - "
A data.frame: 2 × 18
sample_idsampleidmeasurementsc_rna_seq_dataagesexclassificationgroupmeta_dataef_classification_datadelta_ef_value_classclinical_datacomplete_clinical_datamin_1_clinical_valuecytokine_dataneutrophil_dataproteomics_data
<chr><chr><chr><chr><dbl><int><chr><chr><chr><dbl><dbl><chr><dbl><dbl><dbl><dbl><dbl><dbl>
1k1 K1 1 TP0055fvollstaendiger_ausschlussno_ccs10NA10111NA
2k10K1010TP0157mccs ccs 10NA10111 1
\n" - ], - "text/latex": [ - "A data.frame: 2 × 18\n", - "\\begin{tabular}{r|llllllllllllllllll}\n", - " & sample\\_id & sample & id & measurement & sc\\_rna\\_seq\\_data & age & sex & classification & group & meta\\_data & ef\\_classification\\_data & delta\\_ef\\_value\\_class & clinical\\_data & complete\\_clinical\\_data & min\\_1\\_clinical\\_value & cytokine\\_data & neutrophil\\_data & proteomics\\_data\\\\\n", - " & & & & & & & & & & & & & & & & & & \\\\\n", - "\\hline\n", - "\t1 & k1 & K1 & 1 & TP0 & 0 & 55 & f & vollstaendiger\\_ausschluss & no\\_ccs & 1 & 0 & NA & 1 & 0 & 1 & 1 & 1 & NA\\\\\n", - "\t2 & k10 & K10 & 10 & TP0 & 1 & 57 & m & ccs & ccs & 1 & 0 & NA & 1 & 0 & 1 & 1 & 1 & 1\\\\\n", - "\\end{tabular}\n" + "146" ], "text/markdown": [ - "\n", - "A data.frame: 2 × 18\n", - "\n", - "| | sample_id <chr> | sample <chr> | id <chr> | measurement <chr> | sc_rna_seq_data <dbl> | age <int> | sex <chr> | classification <chr> | group <chr> | meta_data <dbl> | ef_classification_data <dbl> | delta_ef_value_class <chr> | clinical_data <dbl> | complete_clinical_data <dbl> | min_1_clinical_value <dbl> | cytokine_data <dbl> | neutrophil_data <dbl> | proteomics_data <dbl> |\n", - "|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|\n", - "| 1 | k1 | K1 | 1 | TP0 | 0 | 55 | f | vollstaendiger_ausschluss | no_ccs | 1 | 0 | NA | 1 | 0 | 1 | 1 | 1 | NA |\n", - "| 2 | k10 | K10 | 10 | TP0 | 1 | 57 | m | ccs | ccs | 1 | 0 | NA | 1 | 0 | 1 | 1 | 1 | 1 |\n", - "\n" + "146" ], "text/plain": [ - " sample_id sample id measurement sc_rna_seq_data age sex\n", - "1 k1 K1 1 TP0 0 55 f \n", - "2 k10 K10 10 TP0 1 57 m \n", - " classification group meta_data ef_classification_data\n", - "1 vollstaendiger_ausschluss no_ccs 1 0 \n", - "2 ccs ccs 1 0 \n", - " delta_ef_value_class clinical_data complete_clinical_data\n", - "1 NA 1 0 \n", - "2 NA 1 0 \n", - " min_1_clinical_value cytokine_data neutrophil_data proteomics_data\n", - "1 1 1 1 NA \n", - "2 1 1 1 1 " + "[1] 146" ] }, "metadata": {}, @@ -6628,7 +5077,7 @@ } ], "source": [ - "head(all_samples_info,2)" + "nrow(all_samples_info)" ] }, { @@ -6670,14 +5119,6 @@ "sum(all_samples_info$proteomics) # 119 sample- tp combinations for which proteomics info can be matched" ] }, - { - "cell_type": "raw", - "id": "8bafe48f-057e-422c-a46a-1d68cb45ae0a", - "metadata": {}, - "source": [ - "Summary: for 119 sample - tp combinations proteomics data is available in the file; M2.3 seems to be twice in the file: M2.3_P10.2, M2.3_P10.3 --> has been removed" - ] - }, { "cell_type": "code", "execution_count": 241, @@ -6799,70 +5240,6 @@ "## Visualize all loaded and available data (heatmap)" ] }, - { - "cell_type": "code", - "execution_count": 246, - "id": "7d7a1433-388f-494f-934b-14f854d49121", - "metadata": {}, - "outputs": [ - { - "data": { - "text/html": [ - "\n", - "\n", - "\n", - "\t\n", - "\t\n", - "\n", - "\n", - "\t\n", - "\t\n", - "\n", - "
A data.frame: 2 × 18
sample_idsampleidmeasurementsc_rna_seq_dataagesexclassificationgroupmeta_dataef_classification_datadelta_ef_value_classclinical_datacomplete_clinical_datamin_1_clinical_valuecytokine_dataneutrophil_dataproteomics_data
<chr><chr><chr><chr><dbl><int><chr><chr><chr><dbl><dbl><chr><dbl><dbl><dbl><dbl><dbl><dbl>
1k1 K1 1 TP0055fvollstaendiger_ausschlussno_ccs10NA101110
2k10K1010TP0157mccs ccs 10NA101111
\n" - ], - "text/latex": [ - "A data.frame: 2 × 18\n", - "\\begin{tabular}{r|llllllllllllllllll}\n", - " & sample\\_id & sample & id & measurement & sc\\_rna\\_seq\\_data & age & sex & classification & group & meta\\_data & ef\\_classification\\_data & delta\\_ef\\_value\\_class & clinical\\_data & complete\\_clinical\\_data & min\\_1\\_clinical\\_value & cytokine\\_data & neutrophil\\_data & proteomics\\_data\\\\\n", - " & & & & & & & & & & & & & & & & & & \\\\\n", - "\\hline\n", - "\t1 & k1 & K1 & 1 & TP0 & 0 & 55 & f & vollstaendiger\\_ausschluss & no\\_ccs & 1 & 0 & NA & 1 & 0 & 1 & 1 & 1 & 0\\\\\n", - "\t2 & k10 & K10 & 10 & TP0 & 1 & 57 & m & ccs & ccs & 1 & 0 & NA & 1 & 0 & 1 & 1 & 1 & 1\\\\\n", - "\\end{tabular}\n" - ], - "text/markdown": [ - "\n", - "A data.frame: 2 × 18\n", - "\n", - "| | sample_id <chr> | sample <chr> | id <chr> | measurement <chr> | sc_rna_seq_data <dbl> | age <int> | sex <chr> | classification <chr> | group <chr> | meta_data <dbl> | ef_classification_data <dbl> | delta_ef_value_class <chr> | clinical_data <dbl> | complete_clinical_data <dbl> | min_1_clinical_value <dbl> | cytokine_data <dbl> | neutrophil_data <dbl> | proteomics_data <dbl> |\n", - "|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|\n", - "| 1 | k1 | K1 | 1 | TP0 | 0 | 55 | f | vollstaendiger_ausschluss | no_ccs | 1 | 0 | NA | 1 | 0 | 1 | 1 | 1 | 0 |\n", - "| 2 | k10 | K10 | 10 | TP0 | 1 | 57 | m | ccs | ccs | 1 | 0 | NA | 1 | 0 | 1 | 1 | 1 | 1 |\n", - "\n" - ], - "text/plain": [ - " sample_id sample id measurement sc_rna_seq_data age sex\n", - "1 k1 K1 1 TP0 0 55 f \n", - "2 k10 K10 10 TP0 1 57 m \n", - " classification group meta_data ef_classification_data\n", - "1 vollstaendiger_ausschluss no_ccs 1 0 \n", - "2 ccs ccs 1 0 \n", - " delta_ef_value_class clinical_data complete_clinical_data\n", - "1 NA 1 0 \n", - "2 NA 1 0 \n", - " min_1_clinical_value cytokine_data neutrophil_data proteomics_data\n", - "1 1 1 1 0 \n", - "2 1 1 1 1 " - ] - }, - "metadata": {}, - "output_type": "display_data" - } - ], - "source": [ - "head(all_samples_info,2)" - ] - }, { "cell_type": "code", "execution_count": 247, @@ -6901,64 +5278,6 @@ "heatmap_overview = melt(all_samples_info, id.vars = c('sample_id', 'sample', 'id', 'measurement', 'age', 'sex', 'classification', 'group', 'delta_ef_value_class'), variable.name = 'data_source')" ] }, - { - "cell_type": "code", - "execution_count": 250, - "id": "b59e1744-1858-4d4e-af72-b379a3786afb", - "metadata": {}, - "outputs": [ - { - "data": { - "text/html": [ - "\n", - "\n", - "\n", - "\t\n", - "\t\n", - "\n", - "\n", - "\t\n", - "\t\n", - "\n", - "
A data.frame: 2 × 11
sample_idsampleidmeasurementagesexclassificationgroupdelta_ef_value_classdata_sourcevalue
<chr><chr><chr><chr><int><chr><chr><chr><chr><fct><dbl>
1k1 K1 1 TP055fvollstaendiger_ausschlussno_ccs-sc_rna_seq_data0
2k10K1010TP057mccs ccs -sc_rna_seq_data1
\n" - ], - "text/latex": [ - "A data.frame: 2 × 11\n", - "\\begin{tabular}{r|lllllllllll}\n", - " & sample\\_id & sample & id & measurement & age & sex & classification & group & delta\\_ef\\_value\\_class & data\\_source & value\\\\\n", - " & & & & & & & & & & & \\\\\n", - "\\hline\n", - "\t1 & k1 & K1 & 1 & TP0 & 55 & f & vollstaendiger\\_ausschluss & no\\_ccs & - & sc\\_rna\\_seq\\_data & 0\\\\\n", - "\t2 & k10 & K10 & 10 & TP0 & 57 & m & ccs & ccs & - & sc\\_rna\\_seq\\_data & 1\\\\\n", - "\\end{tabular}\n" - ], - "text/markdown": [ - "\n", - "A data.frame: 2 × 11\n", - "\n", - "| | sample_id <chr> | sample <chr> | id <chr> | measurement <chr> | age <int> | sex <chr> | classification <chr> | group <chr> | delta_ef_value_class <chr> | data_source <fct> | value <dbl> |\n", - "|---|---|---|---|---|---|---|---|---|---|---|---|\n", - "| 1 | k1 | K1 | 1 | TP0 | 55 | f | vollstaendiger_ausschluss | no_ccs | - | sc_rna_seq_data | 0 |\n", - "| 2 | k10 | K10 | 10 | TP0 | 57 | m | ccs | ccs | - | sc_rna_seq_data | 1 |\n", - "\n" - ], - "text/plain": [ - " sample_id sample id measurement age sex classification group \n", - "1 k1 K1 1 TP0 55 f vollstaendiger_ausschluss no_ccs\n", - "2 k10 K10 10 TP0 57 m ccs ccs \n", - " delta_ef_value_class data_source value\n", - "1 - sc_rna_seq_data 0 \n", - "2 - sc_rna_seq_data 1 " - ] - }, - "metadata": {}, - "output_type": "display_data" - } - ], - "source": [ - "head(heatmap_overview,2)" - ] - }, { "cell_type": "code", "execution_count": 251, @@ -7494,70 +5813,6 @@ "### Overview of available data and missing data per sample" ] }, - { - "cell_type": "code", - "execution_count": 264, - "id": "6b8db476-7911-4650-86d4-28a9495c88a8", - "metadata": {}, - "outputs": [ - { - "data": { - "text/html": [ - "\n", - "\n", - "\n", - "\t\n", - "\t\n", - "\n", - "\n", - "\t\n", - "\t\n", - "\n", - "
A data.frame: 2 × 18
sample_idsampleidmeasurementsc_rna_seq_dataagesexclassificationgroupmeta_dataef_classification_datadelta_ef_value_classclinical_datacomplete_clinical_datamin_1_clinical_valuecytokine_dataneutrophil_dataproteomics_data
<chr><chr><chr><chr><dbl><int><chr><chr><chr><dbl><dbl><chr><dbl><dbl><dbl><dbl><dbl><dbl>
1k1 K1 1 TP0055fvollstaendiger_ausschlussno_ccs10-101110
2k10K1010TP0157mccs ccs 10-101111
\n" - ], - "text/latex": [ - "A data.frame: 2 × 18\n", - "\\begin{tabular}{r|llllllllllllllllll}\n", - " & sample\\_id & sample & id & measurement & sc\\_rna\\_seq\\_data & age & sex & classification & group & meta\\_data & ef\\_classification\\_data & delta\\_ef\\_value\\_class & clinical\\_data & complete\\_clinical\\_data & min\\_1\\_clinical\\_value & cytokine\\_data & neutrophil\\_data & proteomics\\_data\\\\\n", - " & & & & & & & & & & & & & & & & & & \\\\\n", - "\\hline\n", - "\t1 & k1 & K1 & 1 & TP0 & 0 & 55 & f & vollstaendiger\\_ausschluss & no\\_ccs & 1 & 0 & - & 1 & 0 & 1 & 1 & 1 & 0\\\\\n", - "\t2 & k10 & K10 & 10 & TP0 & 1 & 57 & m & ccs & ccs & 1 & 0 & - & 1 & 0 & 1 & 1 & 1 & 1\\\\\n", - "\\end{tabular}\n" - ], - "text/markdown": [ - "\n", - "A data.frame: 2 × 18\n", - "\n", - "| | sample_id <chr> | sample <chr> | id <chr> | measurement <chr> | sc_rna_seq_data <dbl> | age <int> | sex <chr> | classification <chr> | group <chr> | meta_data <dbl> | ef_classification_data <dbl> | delta_ef_value_class <chr> | clinical_data <dbl> | complete_clinical_data <dbl> | min_1_clinical_value <dbl> | cytokine_data <dbl> | neutrophil_data <dbl> | proteomics_data <dbl> |\n", - "|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|\n", - "| 1 | k1 | K1 | 1 | TP0 | 0 | 55 | f | vollstaendiger_ausschluss | no_ccs | 1 | 0 | - | 1 | 0 | 1 | 1 | 1 | 0 |\n", - "| 2 | k10 | K10 | 10 | TP0 | 1 | 57 | m | ccs | ccs | 1 | 0 | - | 1 | 0 | 1 | 1 | 1 | 1 |\n", - "\n" - ], - "text/plain": [ - " sample_id sample id measurement sc_rna_seq_data age sex\n", - "1 k1 K1 1 TP0 0 55 f \n", - "2 k10 K10 10 TP0 1 57 m \n", - " classification group meta_data ef_classification_data\n", - "1 vollstaendiger_ausschluss no_ccs 1 0 \n", - "2 ccs ccs 1 0 \n", - " delta_ef_value_class clinical_data complete_clinical_data\n", - "1 - 1 0 \n", - "2 - 1 0 \n", - " min_1_clinical_value cytokine_data neutrophil_data proteomics_data\n", - "1 1 1 1 0 \n", - "2 1 1 1 1 " - ] - }, - "metadata": {}, - "output_type": "display_data" - } - ], - "source": [ - "head(all_samples_info,2)" - ] - }, { "cell_type": "code", "execution_count": 265, @@ -7618,70 +5873,6 @@ "### Merged Sample Data Meta-Data file" ] }, - { - "cell_type": "code", - "execution_count": 269, - "id": "89fd1739-3517-4a92-9cbe-f77187b68e87", - "metadata": {}, - "outputs": [ - { - "data": { - "text/html": [ - "\n", - "\n", - "\n", - "\t\n", - "\t\n", - "\n", - "\n", - "\t\n", - "\t\n", - "\n", - "
A data.frame: 2 × 31
sample_idsampleidmeasurementlibraryid.ynamereadpatternsequence⋯delta_ef_valuedelta_ef_value_classef_classification_dataCKCK_MBTroponinCRPclinical_datacomplete_clinical_datamin_1_clinical_value
<chr><chr><chr><chr><chr><chr><chr><chr><chr><chr>⋯<dbl><chr><dbl><int><chr><dbl><chr><dbl><dbl><dbl>
1k1 K1 1 TP0L13HTO_B0251No-CCS-1 R25PNNNNNNNNNN(BC)GTCAACTCTTTAGCG⋯NANA0430.0130.4101
2k10K1010TP0L11HTO_B0256Ch-CCS-10R25PNNNNNNNNNN(BC)GGTTGCCAGATGTCA⋯NANA0NA NA0.2101
\n" - ], - "text/latex": [ - "A data.frame: 2 × 31\n", - "\\begin{tabular}{r|lllllllllllllllllllll}\n", - " & sample\\_id & sample & id & measurement & library & id.y & name & read & pattern & sequence & ⋯ & delta\\_ef\\_value & delta\\_ef\\_value\\_class & ef\\_classification\\_data & CK & CK\\_MB & Troponin & CRP & clinical\\_data & complete\\_clinical\\_data & min\\_1\\_clinical\\_value\\\\\n", - " & & & & & & & & & & & ⋯ & & & & & & & & & & \\\\\n", - "\\hline\n", - "\t1 & k1 & K1 & 1 & TP0 & L13 & HTO\\_B0251 & No-CCS-1 & R2 & 5PNNNNNNNNNN(BC) & GTCAACTCTTTAGCG & ⋯ & NA & NA & 0 & 43 & & 0.013 & 0.4 & 1 & 0 & 1\\\\\n", - "\t2 & k10 & K10 & 10 & TP0 & L11 & HTO\\_B0256 & Ch-CCS-10 & R2 & 5PNNNNNNNNNN(BC) & GGTTGCCAGATGTCA & ⋯ & NA & NA & 0 & NA & & NA & 0.2 & 1 & 0 & 1\\\\\n", - "\\end{tabular}\n" - ], - "text/markdown": [ - "\n", - "A data.frame: 2 × 31\n", - "\n", - "| | sample_id <chr> | sample <chr> | id <chr> | measurement <chr> | library <chr> | id.y <chr> | name <chr> | read <chr> | pattern <chr> | sequence <chr> | ⋯ ⋯ | delta_ef_value <dbl> | delta_ef_value_class <chr> | ef_classification_data <dbl> | CK <int> | CK_MB <chr> | Troponin <dbl> | CRP <chr> | clinical_data <dbl> | complete_clinical_data <dbl> | min_1_clinical_value <dbl> |\n", - "|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|\n", - "| 1 | k1 | K1 | 1 | TP0 | L13 | HTO_B0251 | No-CCS-1 | R2 | 5PNNNNNNNNNN(BC) | GTCAACTCTTTAGCG | ⋯ | NA | NA | 0 | 43 | | 0.013 | 0.4 | 1 | 0 | 1 |\n", - "| 2 | k10 | K10 | 10 | TP0 | L11 | HTO_B0256 | Ch-CCS-10 | R2 | 5PNNNNNNNNNN(BC) | GGTTGCCAGATGTCA | ⋯ | NA | NA | 0 | NA | | NA | 0.2 | 1 | 0 | 1 |\n", - "\n" - ], - "text/plain": [ - " sample_id sample id measurement library id.y name read\n", - "1 k1 K1 1 TP0 L13 HTO_B0251 No-CCS-1 R2 \n", - "2 k10 K10 10 TP0 L11 HTO_B0256 Ch-CCS-10 R2 \n", - " pattern sequence ⋯ delta_ef_value delta_ef_value_class\n", - "1 5PNNNNNNNNNN(BC) GTCAACTCTTTAGCG ⋯ NA NA \n", - "2 5PNNNNNNNNNN(BC) GGTTGCCAGATGTCA ⋯ NA NA \n", - " ef_classification_data CK CK_MB Troponin CRP clinical_data\n", - "1 0 43 0.013 0.4 1 \n", - "2 0 NA NA 0.2 1 \n", - " complete_clinical_data min_1_clinical_value\n", - "1 0 1 \n", - "2 0 1 " - ] - }, - "metadata": {}, - "output_type": "display_data" - } - ], - "source": [ - "head(sample_data,2)" - ] - }, { "cell_type": "code", "execution_count": 270, @@ -8032,139 +6223,28 @@ "| | SERPINA1_A0A024R6I7 <dbl> | IGLV4.69_A0A075B6H9 <dbl> | IGLV8.61_A0A075B6I0 <dbl> | IGLV4.60_A0A075B6I1 <dbl> | IGLV10.54_A0A075B6I4 <dbl> | IGLV7.46_A0A075B6I9 <dbl> | IGLV2.18_A0A075B6J9 <dbl> | IGLV3.16_A0A075B6K0 <dbl> | IGLV3.12_A0A075B6K2 <dbl> | IGLV3.10_A0A075B6K4 <dbl> | ⋯ ⋯ | MINPP1_Q9UNW1 <dbl> | TLN1_Q9Y490 <dbl> | ANGPTL3_Q9Y5C1 <dbl> | LYVE1_Q9Y5Y7 <dbl> | FCGBP_Q9Y6R7 <dbl> | COLEC10_Q9Y6Z7 <dbl> | IGHV3OR16.9_S4R460 <dbl> | APOA2_V9GYM3 <dbl> | sample_id <chr> | proteomics_data <dbl> |\n", "|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|\n", "| M2.3_P10.2 | -1.663380 | -2.414588 | 1.467756 | -6.164178 | -1.858412 | -2.588001 | 2.128858 | -0.110549 | 1.968863 | 2.523862 | ⋯ | 4.3852723 | -2.882139 | -6.1443596 | -4.26206 | 0.1977374 | -1.653755 | 6.184887 | 4.235612 | m2.3 | 1 |\n", - "| M5.1_P1 | 3.744514 | -2.672991 | 2.308556 | -5.999634 | -3.812528 | -2.425649 | 1.186534 | -2.204914 | 1.172303 | 1.799312 | ⋯ | -0.5717449 | -3.766868 | 0.4187132 | -5.92088 | -0.1863114 | -1.655054 | 6.121172 | 4.837075 | m5.1 | 1 |\n", - "\n" - ], - "text/plain": [ - " SERPINA1_A0A024R6I7 IGLV4.69_A0A075B6H9 IGLV8.61_A0A075B6I0\n", - "M2.3_P10.2 -1.663380 -2.414588 1.467756 \n", - "M5.1_P1 3.744514 -2.672991 2.308556 \n", - " IGLV4.60_A0A075B6I1 IGLV10.54_A0A075B6I4 IGLV7.46_A0A075B6I9\n", - "M2.3_P10.2 -6.164178 -1.858412 -2.588001 \n", - "M5.1_P1 -5.999634 -3.812528 -2.425649 \n", - " IGLV2.18_A0A075B6J9 IGLV3.16_A0A075B6K0 IGLV3.12_A0A075B6K2\n", - "M2.3_P10.2 2.128858 -0.110549 1.968863 \n", - "M5.1_P1 1.186534 -2.204914 1.172303 \n", - " IGLV3.10_A0A075B6K4 ⋯ MINPP1_Q9UNW1 TLN1_Q9Y490 ANGPTL3_Q9Y5C1\n", - "M2.3_P10.2 2.523862 ⋯ 4.3852723 -2.882139 -6.1443596 \n", - "M5.1_P1 1.799312 ⋯ -0.5717449 -3.766868 0.4187132 \n", - " LYVE1_Q9Y5Y7 FCGBP_Q9Y6R7 COLEC10_Q9Y6Z7 IGHV3OR16.9_S4R460\n", - "M2.3_P10.2 -4.26206 0.1977374 -1.653755 6.184887 \n", - "M5.1_P1 -5.92088 -0.1863114 -1.655054 6.121172 \n", - " APOA2_V9GYM3 sample_id proteomics_data\n", - "M2.3_P10.2 4.235612 m2.3 1 \n", - "M5.1_P1 4.837075 m5.1 1 " - ] - }, - "metadata": {}, - "output_type": "display_data" - } - ], - "source": [ - "head(proteomics,2)" - ] - }, - { - "cell_type": "code", - "execution_count": 285, - "id": "9acb97ef-421e-46b9-b441-4eddaeeb52c8", - "metadata": {}, - "outputs": [ - { - "data": { - "text/html": [ - "119" - ], - "text/latex": [ - "119" - ], - "text/markdown": [ - "119" - ], - "text/plain": [ - "[1] 119" - ] - }, - "metadata": {}, - "output_type": "display_data" - } - ], - "source": [ - "nrow(proteomics) # 119 matchable sample-ids" - ] - }, - { - "cell_type": "code", - "execution_count": 286, - "id": "14333b7f-3372-4525-ad8c-81c679798db7", - "metadata": {}, - "outputs": [], - "source": [ - "write.csv(proteomics, paste0(result_path, '/00_Data_Overview/Prepared_Proteomic_Data.csv'))" - ] - }, - { - "cell_type": "markdown", - "id": "6997a181-04ff-415c-8eca-c97713f66af9", - "metadata": {}, - "source": [ - "# Save sample data for paper supplementary table" - ] - }, - { - "cell_type": "code", - "execution_count": 287, - "id": "0fbb8540-3a27-454d-9ea5-56633f482b9b", - "metadata": {}, - "outputs": [ - { - "data": { - "text/html": [ - "\n", - "\n", - "\n", - "\t\n", - "\t\n", - "\n", - "\n", - "\t\n", - "\t\n", - "\n", - "
A data.frame: 2 × 29
sample_idsampleidmeasurementlibraryid.ynamereadpatternsequence⋯meta_datadelta_ef_value_groupdelta_ef_valuedelta_ef_value_classef_classification_dataCKCK_MBTroponinCRPclinical_data
<chr><chr><chr><chr><chr><chr><chr><chr><chr><chr>⋯<dbl><chr><dbl><chr><dbl><int><chr><dbl><chr><dbl>
1k1 K1 1 TP0L13HTO_B0251No-CCS-1 R25PNNNNNNNNNN(BC)GTCAACTCTTTAGCG⋯1NANANA0430.0130.41
2k10K1010TP0L11HTO_B0256Ch-CCS-10R25PNNNNNNNNNN(BC)GGTTGCCAGATGTCA⋯1NANANA0NA NA0.21
\n" - ], - "text/latex": [ - "A data.frame: 2 × 29\n", - "\\begin{tabular}{r|lllllllllllllllllllll}\n", - " & sample\\_id & sample & id & measurement & library & id.y & name & read & pattern & sequence & ⋯ & meta\\_data & delta\\_ef\\_value\\_group & delta\\_ef\\_value & delta\\_ef\\_value\\_class & ef\\_classification\\_data & CK & CK\\_MB & Troponin & CRP & clinical\\_data\\\\\n", - " & & & & & & & & & & & ⋯ & & & & & & & & & & \\\\\n", - "\\hline\n", - "\t1 & k1 & K1 & 1 & TP0 & L13 & HTO\\_B0251 & No-CCS-1 & R2 & 5PNNNNNNNNNN(BC) & GTCAACTCTTTAGCG & ⋯ & 1 & NA & NA & NA & 0 & 43 & & 0.013 & 0.4 & 1\\\\\n", - "\t2 & k10 & K10 & 10 & TP0 & L11 & HTO\\_B0256 & Ch-CCS-10 & R2 & 5PNNNNNNNNNN(BC) & GGTTGCCAGATGTCA & ⋯ & 1 & NA & NA & NA & 0 & NA & & NA & 0.2 & 1\\\\\n", - "\\end{tabular}\n" - ], - "text/markdown": [ - "\n", - "A data.frame: 2 × 29\n", - "\n", - "| | sample_id <chr> | sample <chr> | id <chr> | measurement <chr> | library <chr> | id.y <chr> | name <chr> | read <chr> | pattern <chr> | sequence <chr> | ⋯ ⋯ | meta_data <dbl> | delta_ef_value_group <chr> | delta_ef_value <dbl> | delta_ef_value_class <chr> | ef_classification_data <dbl> | CK <int> | CK_MB <chr> | Troponin <dbl> | CRP <chr> | clinical_data <dbl> |\n", - "|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|\n", - "| 1 | k1 | K1 | 1 | TP0 | L13 | HTO_B0251 | No-CCS-1 | R2 | 5PNNNNNNNNNN(BC) | GTCAACTCTTTAGCG | ⋯ | 1 | NA | NA | NA | 0 | 43 | | 0.013 | 0.4 | 1 |\n", - "| 2 | k10 | K10 | 10 | TP0 | L11 | HTO_B0256 | Ch-CCS-10 | R2 | 5PNNNNNNNNNN(BC) | GGTTGCCAGATGTCA | ⋯ | 1 | NA | NA | NA | 0 | NA | | NA | 0.2 | 1 |\n", + "| M5.1_P1 | 3.744514 | -2.672991 | 2.308556 | -5.999634 | -3.812528 | -2.425649 | 1.186534 | -2.204914 | 1.172303 | 1.799312 | ⋯ | -0.5717449 | -3.766868 | 0.4187132 | -5.92088 | -0.1863114 | -1.655054 | 6.121172 | 4.837075 | m5.1 | 1 |\n", "\n" ], "text/plain": [ - " sample_id sample id measurement library id.y name read\n", - "1 k1 K1 1 TP0 L13 HTO_B0251 No-CCS-1 R2 \n", - "2 k10 K10 10 TP0 L11 HTO_B0256 Ch-CCS-10 R2 \n", - " pattern sequence ⋯ meta_data delta_ef_value_group\n", - "1 5PNNNNNNNNNN(BC) GTCAACTCTTTAGCG ⋯ 1 NA \n", - "2 5PNNNNNNNNNN(BC) GGTTGCCAGATGTCA ⋯ 1 NA \n", - " delta_ef_value delta_ef_value_class ef_classification_data CK CK_MB Troponin\n", - "1 NA NA 0 43 0.013 \n", - "2 NA NA 0 NA NA \n", - " CRP clinical_data\n", - "1 0.4 1 \n", - "2 0.2 1 " + " SERPINA1_A0A024R6I7 IGLV4.69_A0A075B6H9 IGLV8.61_A0A075B6I0\n", + "M2.3_P10.2 -1.663380 -2.414588 1.467756 \n", + "M5.1_P1 3.744514 -2.672991 2.308556 \n", + " IGLV4.60_A0A075B6I1 IGLV10.54_A0A075B6I4 IGLV7.46_A0A075B6I9\n", + "M2.3_P10.2 -6.164178 -1.858412 -2.588001 \n", + "M5.1_P1 -5.999634 -3.812528 -2.425649 \n", + " IGLV2.18_A0A075B6J9 IGLV3.16_A0A075B6K0 IGLV3.12_A0A075B6K2\n", + "M2.3_P10.2 2.128858 -0.110549 1.968863 \n", + "M5.1_P1 1.186534 -2.204914 1.172303 \n", + " IGLV3.10_A0A075B6K4 ⋯ MINPP1_Q9UNW1 TLN1_Q9Y490 ANGPTL3_Q9Y5C1\n", + "M2.3_P10.2 2.523862 ⋯ 4.3852723 -2.882139 -6.1443596 \n", + "M5.1_P1 1.799312 ⋯ -0.5717449 -3.766868 0.4187132 \n", + " LYVE1_Q9Y5Y7 FCGBP_Q9Y6R7 COLEC10_Q9Y6Z7 IGHV3OR16.9_S4R460\n", + "M2.3_P10.2 -4.26206 0.1977374 -1.653755 6.184887 \n", + "M5.1_P1 -5.92088 -0.1863114 -1.655054 6.121172 \n", + " APOA2_V9GYM3 sample_id proteomics_data\n", + "M2.3_P10.2 4.235612 m2.3 1 \n", + "M5.1_P1 4.837075 m5.1 1 " ] }, "metadata": {}, @@ -8172,63 +6252,28 @@ } ], "source": [ - "head(sample_data,2)" + "head(proteomics,2)" ] }, { "cell_type": "code", - "execution_count": 288, - "id": "9bac334a-61e6-4e67-affe-35194cbc88f2", + "execution_count": 285, + "id": "9acb97ef-421e-46b9-b441-4eddaeeb52c8", "metadata": {}, "outputs": [ { "data": { "text/html": [ - "\n", - "\n", - "\n", - "\t\n", - "\t\n", - "\n", - "\n", - "\t\n", - "\t\n", - "\n", - "
A data.frame: 2 × 16
sample_idsampleidmeasurementsc_rna_seq_dataagesexclassificationgroupmeta_dataef_classification_datadelta_ef_value_classclinical_datacytokine_dataneutrophil_dataproteomics_data
<chr><chr><chr><chr><dbl><int><chr><chr><chr><dbl><dbl><chr><dbl><dbl><dbl><dbl>
1k1 K1 1 TP0055fvollstaendiger_ausschlussno_ccs10-1110
2k10K1010TP0157mccs ccs 10-1111
\n" + "119" ], "text/latex": [ - "A data.frame: 2 × 16\n", - "\\begin{tabular}{r|llllllllllllllll}\n", - " & sample\\_id & sample & id & measurement & sc\\_rna\\_seq\\_data & age & sex & classification & group & meta\\_data & ef\\_classification\\_data & delta\\_ef\\_value\\_class & clinical\\_data & cytokine\\_data & neutrophil\\_data & proteomics\\_data\\\\\n", - " & & & & & & & & & & & & & & & & \\\\\n", - "\\hline\n", - "\t1 & k1 & K1 & 1 & TP0 & 0 & 55 & f & vollstaendiger\\_ausschluss & no\\_ccs & 1 & 0 & - & 1 & 1 & 1 & 0\\\\\n", - "\t2 & k10 & K10 & 10 & TP0 & 1 & 57 & m & ccs & ccs & 1 & 0 & - & 1 & 1 & 1 & 1\\\\\n", - "\\end{tabular}\n" + "119" ], "text/markdown": [ - "\n", - "A data.frame: 2 × 16\n", - "\n", - "| | sample_id <chr> | sample <chr> | id <chr> | measurement <chr> | sc_rna_seq_data <dbl> | age <int> | sex <chr> | classification <chr> | group <chr> | meta_data <dbl> | ef_classification_data <dbl> | delta_ef_value_class <chr> | clinical_data <dbl> | cytokine_data <dbl> | neutrophil_data <dbl> | proteomics_data <dbl> |\n", - "|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|\n", - "| 1 | k1 | K1 | 1 | TP0 | 0 | 55 | f | vollstaendiger_ausschluss | no_ccs | 1 | 0 | - | 1 | 1 | 1 | 0 |\n", - "| 2 | k10 | K10 | 10 | TP0 | 1 | 57 | m | ccs | ccs | 1 | 0 | - | 1 | 1 | 1 | 1 |\n", - "\n" + "119" ], "text/plain": [ - " sample_id sample id measurement sc_rna_seq_data age sex\n", - "1 k1 K1 1 TP0 0 55 f \n", - "2 k10 K10 10 TP0 1 57 m \n", - " classification group meta_data ef_classification_data\n", - "1 vollstaendiger_ausschluss no_ccs 1 0 \n", - "2 ccs ccs 1 0 \n", - " delta_ef_value_class clinical_data cytokine_data neutrophil_data\n", - "1 - 1 1 1 \n", - "2 - 1 1 1 \n", - " proteomics_data\n", - "1 0 \n", - "2 1 " + "[1] 119" ] }, "metadata": {}, @@ -8236,7 +6281,25 @@ } ], "source": [ - "head(all_samples_info,2)" + "nrow(proteomics) # 119 matchable sample-ids" + ] + }, + { + "cell_type": "code", + "execution_count": 286, + "id": "14333b7f-3372-4525-ad8c-81c679798db7", + "metadata": {}, + "outputs": [], + "source": [ + "write.csv(proteomics, paste0(result_path, '/00_Data_Overview/Prepared_Proteomic_Data.csv'))" + ] + }, + { + "cell_type": "markdown", + "id": "6997a181-04ff-415c-8eca-c97713f66af9", + "metadata": {}, + "source": [ + "# Save sample data for paper supplementary table" ] }, { @@ -8549,192 +6612,6 @@ "colnames(share_sample_data) = c('sample_id', 'sample', 'id', 'measurement', 'library', 'hashtag', 'read', 'pattern', 'sequence', 'age', 'sex', 'classification', 'group', 'delta_ef_value_group', 'delta_ef_value', 'delta_ef_value_class', 'CK', 'CK_MB', 'Troponin', 'CRP') " ] }, - { - "cell_type": "code", - "execution_count": 297, - "id": "7fb831f0-894b-48fb-aabd-269dbd4ce6d1", - "metadata": {}, - "outputs": [ - { - "data": { - "text/html": [ - "\n", - "\n", - "\n", - "\t\n", - "\t\n", - "\n", - "\n", - "\t\n", - "\t\n", - "\n", - "
A data.frame: 2 × 16
sample_idsampleidmeasurementlibraryhashtagreadpatternsequenceagesexclassificationgroupdelta_ef_value_groupdelta_ef_valuedelta_ef_value_class
<chr><chr><chr><chr><chr><chr><chr><chr><chr><int><chr><chr><chr><chr><dbl><chr>
1k1 K1 1 TP0L13HTO_B0251R25PNNNNNNNNNN(BC)GTCAACTCTTTAGCG55fvollstaendiger_ausschlussno_ccsNANANA
2k10K1010TP0L11HTO_B0256R25PNNNNNNNNNN(BC)GGTTGCCAGATGTCA57mccs ccs NANANA
\n" - ], - "text/latex": [ - "A data.frame: 2 × 16\n", - "\\begin{tabular}{r|llllllllllllllll}\n", - " & sample\\_id & sample & id & measurement & library & hashtag & read & pattern & sequence & age & sex & classification & group & delta\\_ef\\_value\\_group & delta\\_ef\\_value & delta\\_ef\\_value\\_class\\\\\n", - " & & & & & & & & & & & & & & & & \\\\\n", - "\\hline\n", - "\t1 & k1 & K1 & 1 & TP0 & L13 & HTO\\_B0251 & R2 & 5PNNNNNNNNNN(BC) & GTCAACTCTTTAGCG & 55 & f & vollstaendiger\\_ausschluss & no\\_ccs & NA & NA & NA\\\\\n", - "\t2 & k10 & K10 & 10 & TP0 & L11 & HTO\\_B0256 & R2 & 5PNNNNNNNNNN(BC) & GGTTGCCAGATGTCA & 57 & m & ccs & ccs & NA & NA & NA\\\\\n", - "\\end{tabular}\n" - ], - "text/markdown": [ - "\n", - "A data.frame: 2 × 16\n", - "\n", - "| | sample_id <chr> | sample <chr> | id <chr> | measurement <chr> | library <chr> | hashtag <chr> | read <chr> | pattern <chr> | sequence <chr> | age <int> | sex <chr> | classification <chr> | group <chr> | delta_ef_value_group <chr> | delta_ef_value <dbl> | delta_ef_value_class <chr> |\n", - "|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|\n", - "| 1 | k1 | K1 | 1 | TP0 | L13 | HTO_B0251 | R2 | 5PNNNNNNNNNN(BC) | GTCAACTCTTTAGCG | 55 | f | vollstaendiger_ausschluss | no_ccs | NA | NA | NA |\n", - "| 2 | k10 | K10 | 10 | TP0 | L11 | HTO_B0256 | R2 | 5PNNNNNNNNNN(BC) | GGTTGCCAGATGTCA | 57 | m | ccs | ccs | NA | NA | NA |\n", - "\n" - ], - "text/plain": [ - " sample_id sample id measurement library hashtag read pattern \n", - "1 k1 K1 1 TP0 L13 HTO_B0251 R2 5PNNNNNNNNNN(BC)\n", - "2 k10 K10 10 TP0 L11 HTO_B0256 R2 5PNNNNNNNNNN(BC)\n", - " sequence age sex classification group delta_ef_value_group\n", - "1 GTCAACTCTTTAGCG 55 f vollstaendiger_ausschluss no_ccs NA \n", - "2 GGTTGCCAGATGTCA 57 m ccs ccs NA \n", - " delta_ef_value delta_ef_value_class\n", - "1 NA NA \n", - "2 NA NA " - ] - }, - "metadata": {}, - "output_type": "display_data" - } - ], - "source": [ - "head(supp_sample_data,2)" - ] - }, - { - "cell_type": "code", - "execution_count": 298, - "id": "5b1bdfe4-8cda-4de0-868d-8ac36167c88b", - "metadata": {}, - "outputs": [ - { - "data": { - "text/html": [ - "\n", - "\n", - "\n", - "\t\n", - "\t\n", - "\n", - "\n", - "\t\n", - "\t\n", - "\n", - "
A data.frame: 2 × 20
sample_idsampleidmeasurementlibraryhashtagreadpatternsequenceagesexclassificationgroupdelta_ef_value_groupdelta_ef_valuedelta_ef_value_classCKCK_MBTroponinCRP
<chr><chr><chr><chr><chr><chr><chr><chr><chr><int><chr><chr><chr><chr><dbl><chr><int><chr><dbl><chr>
1k1 K1 1 TP0L13HTO_B0251R25PNNNNNNNNNN(BC)GTCAACTCTTTAGCG55fvollstaendiger_ausschlussno_ccsNANANA430.0130.4
2k10K1010TP0L11HTO_B0256R25PNNNNNNNNNN(BC)GGTTGCCAGATGTCA57mccs ccs NANANANA NA0.2
\n" - ], - "text/latex": [ - "A data.frame: 2 × 20\n", - "\\begin{tabular}{r|llllllllllllllllllll}\n", - " & sample\\_id & sample & id & measurement & library & hashtag & read & pattern & sequence & age & sex & classification & group & delta\\_ef\\_value\\_group & delta\\_ef\\_value & delta\\_ef\\_value\\_class & CK & CK\\_MB & Troponin & CRP\\\\\n", - " & & & & & & & & & & & & & & & & & & & & \\\\\n", - "\\hline\n", - "\t1 & k1 & K1 & 1 & TP0 & L13 & HTO\\_B0251 & R2 & 5PNNNNNNNNNN(BC) & GTCAACTCTTTAGCG & 55 & f & vollstaendiger\\_ausschluss & no\\_ccs & NA & NA & NA & 43 & & 0.013 & 0.4\\\\\n", - "\t2 & k10 & K10 & 10 & TP0 & L11 & HTO\\_B0256 & R2 & 5PNNNNNNNNNN(BC) & GGTTGCCAGATGTCA & 57 & m & ccs & ccs & NA & NA & NA & NA & & NA & 0.2\\\\\n", - "\\end{tabular}\n" - ], - "text/markdown": [ - "\n", - "A data.frame: 2 × 20\n", - "\n", - "| | sample_id <chr> | sample <chr> | id <chr> | measurement <chr> | library <chr> | hashtag <chr> | read <chr> | pattern <chr> | sequence <chr> | age <int> | sex <chr> | classification <chr> | group <chr> | delta_ef_value_group <chr> | delta_ef_value <dbl> | delta_ef_value_class <chr> | CK <int> | CK_MB <chr> | Troponin <dbl> | CRP <chr> |\n", - "|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|\n", - "| 1 | k1 | K1 | 1 | TP0 | L13 | HTO_B0251 | R2 | 5PNNNNNNNNNN(BC) | GTCAACTCTTTAGCG | 55 | f | vollstaendiger_ausschluss | no_ccs | NA | NA | NA | 43 | | 0.013 | 0.4 |\n", - "| 2 | k10 | K10 | 10 | TP0 | L11 | HTO_B0256 | R2 | 5PNNNNNNNNNN(BC) | GGTTGCCAGATGTCA | 57 | m | ccs | ccs | NA | NA | NA | NA | | NA | 0.2 |\n", - "\n" - ], - "text/plain": [ - " sample_id sample id measurement library hashtag read pattern \n", - "1 k1 K1 1 TP0 L13 HTO_B0251 R2 5PNNNNNNNNNN(BC)\n", - "2 k10 K10 10 TP0 L11 HTO_B0256 R2 5PNNNNNNNNNN(BC)\n", - " sequence age sex classification group delta_ef_value_group\n", - "1 GTCAACTCTTTAGCG 55 f vollstaendiger_ausschluss no_ccs NA \n", - "2 GGTTGCCAGATGTCA 57 m ccs ccs NA \n", - " delta_ef_value delta_ef_value_class CK CK_MB Troponin CRP\n", - "1 NA NA 43 0.013 0.4\n", - "2 NA NA NA NA 0.2" - ] - }, - "metadata": {}, - "output_type": "display_data" - } - ], - "source": [ - "head(share_sample_data,2)" - ] - }, - { - "cell_type": "code", - "execution_count": 299, - "id": "82df0bc7-af06-47f0-ba1e-fbeb61144ed0", - "metadata": {}, - "outputs": [ - { - "data": { - "text/html": [ - "\n", - "\n", - "\n", - "\t\n", - "\t\n", - "\n", - "\n", - "\t\n", - "\t\n", - "\n", - "
A data.frame: 2 × 16
sample_idsampleidmeasurementsc_rna_seq_dataagesexclassificationgroupmeta_dataef_classification_datadelta_ef_value_classclinical_datacytokine_dataneutrophil_dataproteomics_data
<chr><chr><chr><chr><dbl><int><chr><chr><chr><dbl><dbl><chr><dbl><dbl><dbl><dbl>
1k1 K1 1 TP0055fvollstaendiger_ausschlussno_ccs10-1110
2k10K1010TP0157mccs ccs 10-1111
\n" - ], - "text/latex": [ - "A data.frame: 2 × 16\n", - "\\begin{tabular}{r|llllllllllllllll}\n", - " & sample\\_id & sample & id & measurement & sc\\_rna\\_seq\\_data & age & sex & classification & group & meta\\_data & ef\\_classification\\_data & delta\\_ef\\_value\\_class & clinical\\_data & cytokine\\_data & neutrophil\\_data & proteomics\\_data\\\\\n", - " & & & & & & & & & & & & & & & & \\\\\n", - "\\hline\n", - "\t1 & k1 & K1 & 1 & TP0 & 0 & 55 & f & vollstaendiger\\_ausschluss & no\\_ccs & 1 & 0 & - & 1 & 1 & 1 & 0\\\\\n", - "\t2 & k10 & K10 & 10 & TP0 & 1 & 57 & m & ccs & ccs & 1 & 0 & - & 1 & 1 & 1 & 1\\\\\n", - "\\end{tabular}\n" - ], - "text/markdown": [ - "\n", - "A data.frame: 2 × 16\n", - "\n", - "| | sample_id <chr> | sample <chr> | id <chr> | measurement <chr> | sc_rna_seq_data <dbl> | age <int> | sex <chr> | classification <chr> | group <chr> | meta_data <dbl> | ef_classification_data <dbl> | delta_ef_value_class <chr> | clinical_data <dbl> | cytokine_data <dbl> | neutrophil_data <dbl> | proteomics_data <dbl> |\n", - "|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|\n", - "| 1 | k1 | K1 | 1 | TP0 | 0 | 55 | f | vollstaendiger_ausschluss | no_ccs | 1 | 0 | - | 1 | 1 | 1 | 0 |\n", - "| 2 | k10 | K10 | 10 | TP0 | 1 | 57 | m | ccs | ccs | 1 | 0 | - | 1 | 1 | 1 | 1 |\n", - "\n" - ], - "text/plain": [ - " sample_id sample id measurement sc_rna_seq_data age sex\n", - "1 k1 K1 1 TP0 0 55 f \n", - "2 k10 K10 10 TP0 1 57 m \n", - " classification group meta_data ef_classification_data\n", - "1 vollstaendiger_ausschluss no_ccs 1 0 \n", - "2 ccs ccs 1 0 \n", - " delta_ef_value_class clinical_data cytokine_data neutrophil_data\n", - "1 - 1 1 1 \n", - "2 - 1 1 1 \n", - " proteomics_data\n", - "1 0 \n", - "2 1 " - ] - }, - "metadata": {}, - "output_type": "display_data" - } - ], - "source": [ - "head(all_samples_info,2)" - ] - }, { "cell_type": "code", "execution_count": 300, @@ -8862,131 +6739,6 @@ "nrow(share_sample_data_combined)" ] }, - { - "cell_type": "code", - "execution_count": 305, - "id": "cf07b7db-b941-4d40-992d-1d68b656b64e", - "metadata": {}, - "outputs": [ - { - "data": { - "text/html": [ - "\n", - "\n", - "\n", - "\t\n", - "\t\n", - "\n", - "\n", - "\t\n", - "\t\n", - "\n", - "
A data.frame: 2 × 20
sample_idsampleidmeasurementlibraryhashtagreadpatternsequenceagesexclassificationgroupdelta_ef_value_groupdelta_ef_valuedelta_ef_value_classsc_rna_seq_datacytokine_dataneutrophil_dataproteomics_data
<chr><chr><chr><chr><chr><chr><chr><chr><chr><int><chr><chr><chr><chr><dbl><chr><dbl><dbl><dbl><dbl>
1k1 K1 1 TP0L13HTO_B0251R25PNNNNNNNNNN(BC)GTCAACTCTTTAGCG55fvollstaendiger_ausschlussno_ccsNANANA0110
2k10K1010TP0L11HTO_B0256R25PNNNNNNNNNN(BC)GGTTGCCAGATGTCA57mccs ccs NANANA1111
\n" - ], - "text/latex": [ - "A data.frame: 2 × 20\n", - "\\begin{tabular}{r|llllllllllllllllllll}\n", - " & sample\\_id & sample & id & measurement & library & hashtag & read & pattern & sequence & age & sex & classification & group & delta\\_ef\\_value\\_group & delta\\_ef\\_value & delta\\_ef\\_value\\_class & sc\\_rna\\_seq\\_data & cytokine\\_data & neutrophil\\_data & proteomics\\_data\\\\\n", - " & & & & & & & & & & & & & & & & & & & & \\\\\n", - "\\hline\n", - "\t1 & k1 & K1 & 1 & TP0 & L13 & HTO\\_B0251 & R2 & 5PNNNNNNNNNN(BC) & GTCAACTCTTTAGCG & 55 & f & vollstaendiger\\_ausschluss & no\\_ccs & NA & NA & NA & 0 & 1 & 1 & 0\\\\\n", - "\t2 & k10 & K10 & 10 & TP0 & L11 & HTO\\_B0256 & R2 & 5PNNNNNNNNNN(BC) & GGTTGCCAGATGTCA & 57 & m & ccs & ccs & NA & NA & NA & 1 & 1 & 1 & 1\\\\\n", - "\\end{tabular}\n" - ], - "text/markdown": [ - "\n", - "A data.frame: 2 × 20\n", - "\n", - "| | sample_id <chr> | sample <chr> | id <chr> | measurement <chr> | library <chr> | hashtag <chr> | read <chr> | pattern <chr> | sequence <chr> | age <int> | sex <chr> | classification <chr> | group <chr> | delta_ef_value_group <chr> | delta_ef_value <dbl> | delta_ef_value_class <chr> | sc_rna_seq_data <dbl> | cytokine_data <dbl> | neutrophil_data <dbl> | proteomics_data <dbl> |\n", - "|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|\n", - "| 1 | k1 | K1 | 1 | TP0 | L13 | HTO_B0251 | R2 | 5PNNNNNNNNNN(BC) | GTCAACTCTTTAGCG | 55 | f | vollstaendiger_ausschluss | no_ccs | NA | NA | NA | 0 | 1 | 1 | 0 |\n", - "| 2 | k10 | K10 | 10 | TP0 | L11 | HTO_B0256 | R2 | 5PNNNNNNNNNN(BC) | GGTTGCCAGATGTCA | 57 | m | ccs | ccs | NA | NA | NA | 1 | 1 | 1 | 1 |\n", - "\n" - ], - "text/plain": [ - " sample_id sample id measurement library hashtag read pattern \n", - "1 k1 K1 1 TP0 L13 HTO_B0251 R2 5PNNNNNNNNNN(BC)\n", - "2 k10 K10 10 TP0 L11 HTO_B0256 R2 5PNNNNNNNNNN(BC)\n", - " sequence age sex classification group delta_ef_value_group\n", - "1 GTCAACTCTTTAGCG 55 f vollstaendiger_ausschluss no_ccs NA \n", - "2 GGTTGCCAGATGTCA 57 m ccs ccs NA \n", - " delta_ef_value delta_ef_value_class sc_rna_seq_data cytokine_data\n", - "1 NA NA 0 1 \n", - "2 NA NA 1 1 \n", - " neutrophil_data proteomics_data\n", - "1 1 0 \n", - "2 1 1 " - ] - }, - "metadata": {}, - "output_type": "display_data" - } - ], - "source": [ - "head(supp_sample_data_combined,2)" - ] - }, - { - "cell_type": "code", - "execution_count": 306, - "id": "bf048d65-9299-477e-84cc-6367dd5b0d50", - "metadata": {}, - "outputs": [ - { - "data": { - "text/html": [ - "\n", - "\n", - "\n", - "\t\n", - "\t\n", - "\n", - "\n", - "\t\n", - "\t\n", - "\n", - "
A data.frame: 2 × 24
sample_idsampleidmeasurementlibraryhashtagreadpatternsequenceage⋯delta_ef_valuedelta_ef_value_classCKCK_MBTroponinCRPsc_rna_seq_datacytokine_dataneutrophil_dataproteomics_data
<chr><chr><chr><chr><chr><chr><chr><chr><chr><int>⋯<dbl><chr><int><chr><dbl><chr><dbl><dbl><dbl><dbl>
1k1 K1 1 TP0L13HTO_B0251R25PNNNNNNNNNN(BC)GTCAACTCTTTAGCG55⋯NANA430.0130.40110
2k10K1010TP0L11HTO_B0256R25PNNNNNNNNNN(BC)GGTTGCCAGATGTCA57⋯NANANA NA0.21111
\n" - ], - "text/latex": [ - "A data.frame: 2 × 24\n", - "\\begin{tabular}{r|lllllllllllllllllllll}\n", - " & sample\\_id & sample & id & measurement & library & hashtag & read & pattern & sequence & age & ⋯ & delta\\_ef\\_value & delta\\_ef\\_value\\_class & CK & CK\\_MB & Troponin & CRP & sc\\_rna\\_seq\\_data & cytokine\\_data & neutrophil\\_data & proteomics\\_data\\\\\n", - " & & & & & & & & & & & ⋯ & & & & & & & & & & \\\\\n", - "\\hline\n", - "\t1 & k1 & K1 & 1 & TP0 & L13 & HTO\\_B0251 & R2 & 5PNNNNNNNNNN(BC) & GTCAACTCTTTAGCG & 55 & ⋯ & NA & NA & 43 & & 0.013 & 0.4 & 0 & 1 & 1 & 0\\\\\n", - "\t2 & k10 & K10 & 10 & TP0 & L11 & HTO\\_B0256 & R2 & 5PNNNNNNNNNN(BC) & GGTTGCCAGATGTCA & 57 & ⋯ & NA & NA & NA & & NA & 0.2 & 1 & 1 & 1 & 1\\\\\n", - "\\end{tabular}\n" - ], - "text/markdown": [ - "\n", - "A data.frame: 2 × 24\n", - "\n", - "| | sample_id <chr> | sample <chr> | id <chr> | measurement <chr> | library <chr> | hashtag <chr> | read <chr> | pattern <chr> | sequence <chr> | age <int> | ⋯ ⋯ | delta_ef_value <dbl> | delta_ef_value_class <chr> | CK <int> | CK_MB <chr> | Troponin <dbl> | CRP <chr> | sc_rna_seq_data <dbl> | cytokine_data <dbl> | neutrophil_data <dbl> | proteomics_data <dbl> |\n", - "|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|\n", - "| 1 | k1 | K1 | 1 | TP0 | L13 | HTO_B0251 | R2 | 5PNNNNNNNNNN(BC) | GTCAACTCTTTAGCG | 55 | ⋯ | NA | NA | 43 | | 0.013 | 0.4 | 0 | 1 | 1 | 0 |\n", - "| 2 | k10 | K10 | 10 | TP0 | L11 | HTO_B0256 | R2 | 5PNNNNNNNNNN(BC) | GGTTGCCAGATGTCA | 57 | ⋯ | NA | NA | NA | | NA | 0.2 | 1 | 1 | 1 | 1 |\n", - "\n" - ], - "text/plain": [ - " sample_id sample id measurement library hashtag read pattern \n", - "1 k1 K1 1 TP0 L13 HTO_B0251 R2 5PNNNNNNNNNN(BC)\n", - "2 k10 K10 10 TP0 L11 HTO_B0256 R2 5PNNNNNNNNNN(BC)\n", - " sequence age ⋯ delta_ef_value delta_ef_value_class CK CK_MB Troponin\n", - "1 GTCAACTCTTTAGCG 55 ⋯ NA NA 43 0.013 \n", - "2 GGTTGCCAGATGTCA 57 ⋯ NA NA NA NA \n", - " CRP sc_rna_seq_data cytokine_data neutrophil_data proteomics_data\n", - "1 0.4 0 1 1 0 \n", - "2 0.2 1 1 1 1 " - ] - }, - "metadata": {}, - "output_type": "display_data" - } - ], - "source": [ - "head(share_sample_data_combined,2)" - ] - }, { "cell_type": "code", "execution_count": 307, @@ -9234,129 +6986,6 @@ " " ] }, - { - "cell_type": "code", - "execution_count": 336, - "id": "31750308-8633-4694-b1e9-24a712664b3f", - "metadata": {}, - "outputs": [ - { - "data": { - "text/html": [ - "\n", - "\n", - "\n", - "\t\n", - "\t\n", - "\n", - "\n", - "\t\n", - "\t\n", - "\t\n", - "\t\n", - "\t\n", - "\t\n", - "\t\n", - "\t\n", - "\t\n", - "\t\n", - "\t\n", - "\t\n", - "\t\n", - "\t\n", - "\t\n", - "\n", - "
A grouped_df: 15 × 11
measurementclassificationmean_CKsd_CKmean_CK_MBsd_CK_MBmean_Troponinsd_Troponinmean_CRPsd_CRPamount
<chr><chr><dbl><dbl><dbl><dbl><dbl><dbl><dbl><dbl><int>
TP0ccs 123.3846 57.64336 16.00000 3.5590260.01469231 0.003660251 0.36153850.333012716
TP0koronarsklerose 143.2857 81.12894 29.00000 8.4852810.01857143 0.012673557 0.24000000.2073644 7
TP0vollstaendiger_ausschluss 88.5000 27.22919 NaN NA0.01300000 0.000000000 0.38333330.240138811
TP1acs_subacute 242.5000 164.04369 36.66667 21.7791952.17425000 2.352503401 9.02500006.0895402 4
TP1acs_w_infection 2773.60002375.76447423.60000509.4146646.8516000010.210874243 0.27500000.2217356 5
TP1acs_w_o_infection 1247.11761385.28187216.53846233.1189313.95117647 5.790759992 0.42666670.328343619
TP2acs_subacute 175.0000 113.13708 25.00000 NA1.31650000 1.65957961511.20000005.5154329 4
TP2acs_w_infection 3287.80001953.17145306.40000246.8467147.77600000 4.525249164 2.92500002.2141590 5
TP2acs_w_o_infection 1760.52631404.35772175.26316119.7890934.73310526 5.549764488 0.85714290.747008719
TP3acs_subacute 102.5000 17.67767 NaN NA NaN NA 9.05000004.7376154 4
TP3acs_w_infection 691.8000 559.83274 44.25000 18.0623924.64240000 3.83552718710.92500004.7779877 5
TP3acs_w_o_infection 442.2941 635.03629 46.33333 49.5366412.63937500 2.567088386 3.01875002.627601919
TP4acs_subacute NaN NA NaN NA NaN NA 4.60000004.6669048 4
TP4acs_w_infection 155.5000 89.82019 27.00000 NA3.69675000 3.943798793 4.13333333.2005208 5
TP4acs_w_o_infection 203.4167 181.22836 46.00000 41.0731061.90290000 1.931510431 1.53333331.003743019
\n" - ], - "text/latex": [ - "A grouped\\_df: 15 × 11\n", - "\\begin{tabular}{lllllllllll}\n", - " measurement & classification & mean\\_CK & sd\\_CK & mean\\_CK\\_MB & sd\\_CK\\_MB & mean\\_Troponin & sd\\_Troponin & mean\\_CRP & sd\\_CRP & amount\\\\\n", - " & & & & & & & & & & \\\\\n", - "\\hline\n", - "\t TP0 & ccs & 123.3846 & 57.64336 & 16.00000 & 3.559026 & 0.01469231 & 0.003660251 & 0.3615385 & 0.3330127 & 16\\\\\n", - "\t TP0 & koronarsklerose & 143.2857 & 81.12894 & 29.00000 & 8.485281 & 0.01857143 & 0.012673557 & 0.2400000 & 0.2073644 & 7\\\\\n", - "\t TP0 & vollstaendiger\\_ausschluss & 88.5000 & 27.22919 & NaN & NA & 0.01300000 & 0.000000000 & 0.3833333 & 0.2401388 & 11\\\\\n", - "\t TP1 & acs\\_subacute & 242.5000 & 164.04369 & 36.66667 & 21.779195 & 2.17425000 & 2.352503401 & 9.0250000 & 6.0895402 & 4\\\\\n", - "\t TP1 & acs\\_w\\_infection & 2773.6000 & 2375.76447 & 423.60000 & 509.414664 & 6.85160000 & 10.210874243 & 0.2750000 & 0.2217356 & 5\\\\\n", - "\t TP1 & acs\\_w\\_o\\_infection & 1247.1176 & 1385.28187 & 216.53846 & 233.118931 & 3.95117647 & 5.790759992 & 0.4266667 & 0.3283436 & 19\\\\\n", - "\t TP2 & acs\\_subacute & 175.0000 & 113.13708 & 25.00000 & NA & 1.31650000 & 1.659579615 & 11.2000000 & 5.5154329 & 4\\\\\n", - "\t TP2 & acs\\_w\\_infection & 3287.8000 & 1953.17145 & 306.40000 & 246.846714 & 7.77600000 & 4.525249164 & 2.9250000 & 2.2141590 & 5\\\\\n", - "\t TP2 & acs\\_w\\_o\\_infection & 1760.5263 & 1404.35772 & 175.26316 & 119.789093 & 4.73310526 & 5.549764488 & 0.8571429 & 0.7470087 & 19\\\\\n", - "\t TP3 & acs\\_subacute & 102.5000 & 17.67767 & NaN & NA & NaN & NA & 9.0500000 & 4.7376154 & 4\\\\\n", - "\t TP3 & acs\\_w\\_infection & 691.8000 & 559.83274 & 44.25000 & 18.062392 & 4.64240000 & 3.835527187 & 10.9250000 & 4.7779877 & 5\\\\\n", - "\t TP3 & acs\\_w\\_o\\_infection & 442.2941 & 635.03629 & 46.33333 & 49.536641 & 2.63937500 & 2.567088386 & 3.0187500 & 2.6276019 & 19\\\\\n", - "\t TP4 & acs\\_subacute & NaN & NA & NaN & NA & NaN & NA & 4.6000000 & 4.6669048 & 4\\\\\n", - "\t TP4 & acs\\_w\\_infection & 155.5000 & 89.82019 & 27.00000 & NA & 3.69675000 & 3.943798793 & 4.1333333 & 3.2005208 & 5\\\\\n", - "\t TP4 & acs\\_w\\_o\\_infection & 203.4167 & 181.22836 & 46.00000 & 41.073106 & 1.90290000 & 1.931510431 & 1.5333333 & 1.0037430 & 19\\\\\n", - "\\end{tabular}\n" - ], - "text/markdown": [ - "\n", - "A grouped_df: 15 × 11\n", - "\n", - "| measurement <chr> | classification <chr> | mean_CK <dbl> | sd_CK <dbl> | mean_CK_MB <dbl> | sd_CK_MB <dbl> | mean_Troponin <dbl> | sd_Troponin <dbl> | mean_CRP <dbl> | sd_CRP <dbl> | amount <int> |\n", - "|---|---|---|---|---|---|---|---|---|---|---|\n", - "| TP0 | ccs | 123.3846 | 57.64336 | 16.00000 | 3.559026 | 0.01469231 | 0.003660251 | 0.3615385 | 0.3330127 | 16 |\n", - "| TP0 | koronarsklerose | 143.2857 | 81.12894 | 29.00000 | 8.485281 | 0.01857143 | 0.012673557 | 0.2400000 | 0.2073644 | 7 |\n", - "| TP0 | vollstaendiger_ausschluss | 88.5000 | 27.22919 | NaN | NA | 0.01300000 | 0.000000000 | 0.3833333 | 0.2401388 | 11 |\n", - "| TP1 | acs_subacute | 242.5000 | 164.04369 | 36.66667 | 21.779195 | 2.17425000 | 2.352503401 | 9.0250000 | 6.0895402 | 4 |\n", - "| TP1 | acs_w_infection | 2773.6000 | 2375.76447 | 423.60000 | 509.414664 | 6.85160000 | 10.210874243 | 0.2750000 | 0.2217356 | 5 |\n", - "| TP1 | acs_w_o_infection | 1247.1176 | 1385.28187 | 216.53846 | 233.118931 | 3.95117647 | 5.790759992 | 0.4266667 | 0.3283436 | 19 |\n", - "| TP2 | acs_subacute | 175.0000 | 113.13708 | 25.00000 | NA | 1.31650000 | 1.659579615 | 11.2000000 | 5.5154329 | 4 |\n", - "| TP2 | acs_w_infection | 3287.8000 | 1953.17145 | 306.40000 | 246.846714 | 7.77600000 | 4.525249164 | 2.9250000 | 2.2141590 | 5 |\n", - "| TP2 | acs_w_o_infection | 1760.5263 | 1404.35772 | 175.26316 | 119.789093 | 4.73310526 | 5.549764488 | 0.8571429 | 0.7470087 | 19 |\n", - "| TP3 | acs_subacute | 102.5000 | 17.67767 | NaN | NA | NaN | NA | 9.0500000 | 4.7376154 | 4 |\n", - "| TP3 | acs_w_infection | 691.8000 | 559.83274 | 44.25000 | 18.062392 | 4.64240000 | 3.835527187 | 10.9250000 | 4.7779877 | 5 |\n", - "| TP3 | acs_w_o_infection | 442.2941 | 635.03629 | 46.33333 | 49.536641 | 2.63937500 | 2.567088386 | 3.0187500 | 2.6276019 | 19 |\n", - "| TP4 | acs_subacute | NaN | NA | NaN | NA | NaN | NA | 4.6000000 | 4.6669048 | 4 |\n", - "| TP4 | acs_w_infection | 155.5000 | 89.82019 | 27.00000 | NA | 3.69675000 | 3.943798793 | 4.1333333 | 3.2005208 | 5 |\n", - "| TP4 | acs_w_o_infection | 203.4167 | 181.22836 | 46.00000 | 41.073106 | 1.90290000 | 1.931510431 | 1.5333333 | 1.0037430 | 19 |\n", - "\n" - ], - "text/plain": [ - " measurement classification mean_CK sd_CK mean_CK_MB\n", - "1 TP0 ccs 123.3846 57.64336 16.00000 \n", - "2 TP0 koronarsklerose 143.2857 81.12894 29.00000 \n", - "3 TP0 vollstaendiger_ausschluss 88.5000 27.22919 NaN \n", - "4 TP1 acs_subacute 242.5000 164.04369 36.66667 \n", - "5 TP1 acs_w_infection 2773.6000 2375.76447 423.60000 \n", - "6 TP1 acs_w_o_infection 1247.1176 1385.28187 216.53846 \n", - "7 TP2 acs_subacute 175.0000 113.13708 25.00000 \n", - "8 TP2 acs_w_infection 3287.8000 1953.17145 306.40000 \n", - "9 TP2 acs_w_o_infection 1760.5263 1404.35772 175.26316 \n", - "10 TP3 acs_subacute 102.5000 17.67767 NaN \n", - "11 TP3 acs_w_infection 691.8000 559.83274 44.25000 \n", - "12 TP3 acs_w_o_infection 442.2941 635.03629 46.33333 \n", - "13 TP4 acs_subacute NaN NA NaN \n", - "14 TP4 acs_w_infection 155.5000 89.82019 27.00000 \n", - "15 TP4 acs_w_o_infection 203.4167 181.22836 46.00000 \n", - " sd_CK_MB mean_Troponin sd_Troponin mean_CRP sd_CRP amount\n", - "1 3.559026 0.01469231 0.003660251 0.3615385 0.3330127 16 \n", - "2 8.485281 0.01857143 0.012673557 0.2400000 0.2073644 7 \n", - "3 NA 0.01300000 0.000000000 0.3833333 0.2401388 11 \n", - "4 21.779195 2.17425000 2.352503401 9.0250000 6.0895402 4 \n", - "5 509.414664 6.85160000 10.210874243 0.2750000 0.2217356 5 \n", - "6 233.118931 3.95117647 5.790759992 0.4266667 0.3283436 19 \n", - "7 NA 1.31650000 1.659579615 11.2000000 5.5154329 4 \n", - "8 246.846714 7.77600000 4.525249164 2.9250000 2.2141590 5 \n", - "9 119.789093 4.73310526 5.549764488 0.8571429 0.7470087 19 \n", - "10 NA NaN NA 9.0500000 4.7376154 4 \n", - "11 18.062392 4.64240000 3.835527187 10.9250000 4.7779877 5 \n", - "12 49.536641 2.63937500 2.567088386 3.0187500 2.6276019 19 \n", - "13 NA NaN NA 4.6000000 4.6669048 4 \n", - "14 NA 3.69675000 3.943798793 4.1333333 3.2005208 5 \n", - "15 41.073106 1.90290000 1.931510431 1.5333333 1.0037430 19 " - ] - }, - "metadata": {}, - "output_type": "display_data" - } - ], - "source": [ - "head(summary_data_group,20)" - ] - }, { "cell_type": "code", "execution_count": 578,