From b3656eee10dd5504cb9c3909ed52cc4335f14a00 Mon Sep 17 00:00:00 2001 From: Marina Kan <113850522+marinak-ebi@users.noreply.github.com> Date: Fri, 24 May 2024 14:21:18 +0100 Subject: [PATCH 1/6] Update CategoryMap.conf for "dilated" and "closed" values --- .../DRrequiredAgeingPackage/inst/extdata/CategoryMap.conf | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/Late adults stats pipeline/DRrequiredAgeing/DRrequiredAgeingPackage/inst/extdata/CategoryMap.conf b/Late adults stats pipeline/DRrequiredAgeing/DRrequiredAgeingPackage/inst/extdata/CategoryMap.conf index 1ea8d24a..6b22bc97 100644 --- a/Late adults stats pipeline/DRrequiredAgeing/DRrequiredAgeingPackage/inst/extdata/CategoryMap.conf +++ b/Late adults stats pipeline/DRrequiredAgeing/DRrequiredAgeingPackage/inst/extdata/CategoryMap.conf @@ -10,4 +10,8 @@ no data left eye, present right eye:present right eye no data right eye, present left eye:present left eye no data left eye, right eye abnormal:right eye abnormal no data right eye, left eye abnormal:left eye abnormal +no data right eye, left eye dilated:left eye dilated +no data left eye, right eye dilated:right eye dilated +no data right eye, left eye closed:left eye closed +no data left eye, right eye closed:right eye closed Is_this_file_finished_with_a_new_line_question_mark:0 From b70735e87f934d17c68978912fe314605a2794de Mon Sep 17 00:00:00 2001 From: Marina Kan <113850522+marinak-ebi@users.noreply.github.com> Date: Fri, 24 May 2024 14:22:09 +0100 Subject: [PATCH 2/6] Update MergeParameterList.txt for new EYE parameters --- .../inst/extdata/MergeParameterList.txt | 276 ++++++++++++++++++ 1 file changed, 276 insertions(+) diff --git a/Late adults stats pipeline/DRrequiredAgeing/DRrequiredAgeingPackage/inst/extdata/MergeParameterList.txt b/Late adults stats pipeline/DRrequiredAgeing/DRrequiredAgeingPackage/inst/extdata/MergeParameterList.txt index fb9308d5..54c80fad 100644 --- a/Late adults stats pipeline/DRrequiredAgeing/DRrequiredAgeingPackage/inst/extdata/MergeParameterList.txt +++ b/Late adults stats pipeline/DRrequiredAgeing/DRrequiredAgeingPackage/inst/extdata/MergeParameterList.txt @@ -562,3 +562,279 @@ BCMLA_EYE_083_001 BCMLA_EYE_084_001 BCMLA_EYE_085_001 BCMLA_EYE_086_001 +TCPLA_EYE_080_001 +TCPLA_EYE_085_001 +TCPLA_EYE_010_001 +TCPLA_EYE_082_001 +TCPLA_EYE_019_001 +TCPLA_EYE_014_001 +TCPLA_EYE_081_001 +TCPLA_EYE_025_001 +TCPLA_EYE_002_001 +TCPLA_EYE_018_001 +TCPLA_EYE_011_001 +TCPLA_EYE_016_001 +TCPLA_EYE_005_001 +TCPLA_EYE_017_001 +TCPLA_EYE_083_001 +TCPLA_EYE_084_001 +TCPLA_EYE_026_001 +TCPLA_EYE_027_001 +TCPLA_EYE_023_001 +TCPLA_EYE_024_001 +TCPLA_EYE_004_001 +TCPLA_EYE_007_001 +TCPLA_EYE_015_001 +TCPLA_EYE_013_001 +TCPLA_EYE_008_001 +TCPLA_EYE_006_001 +TCPLA_EYE_086_001 +TCPLA_EYE_009_001 +TCPLA_EYE_012_001 +TCPLA_EYE_003_001 +UCDLA_EYE_011_001 +UCDLA_EYE_082_001 +UCDLA_EYE_083_001 +UCDLA_EYE_002_001 +UCDLA_EYE_084_001 +UCDLA_EYE_023_001 +UCDLA_EYE_015_001 +UCDLA_EYE_004_001 +UCDLA_EYE_027_001 +UCDLA_EYE_013_001 +UCDLA_EYE_016_001 +UCDLA_EYE_009_001 +UCDLA_EYE_080_001 +UCDLA_EYE_003_001 +UCDLA_EYE_007_001 +UCDLA_EYE_085_001 +UCDLA_EYE_086_001 +UCDLA_EYE_018_001 +UCDLA_EYE_008_001 +UCDLA_EYE_012_001 +UCDLA_EYE_081_001 +UCDLA_EYE_010_001 +UCDLA_EYE_019_001 +UCDLA_EYE_024_001 +UCDLA_EYE_026_001 +UCDLA_EYE_005_001 +UCDLA_EYE_017_001 +UCDLA_EYE_025_001 +UCDLA_EYE_014_001 +UCDLA_EYE_006_001 +ICSLA_EYE_015_001 +ICSLA_EYE_003_001 +ICSLA_EYE_010_001 +ICSLA_EYE_006_001 +ICSLA_EYE_084_001 +ICSLA_EYE_005_001 +ICSLA_EYE_085_001 +ICSLA_EYE_009_001 +ICSLA_EYE_017_001 +ICSLA_EYE_027_001 +ICSLA_EYE_019_001 +ICSLA_EYE_018_001 +ICSLA_EYE_013_001 +ICSLA_EYE_014_001 +ICSLA_EYE_083_001 +ICSLA_EYE_002_001 +ICSLA_EYE_012_001 +ICSLA_EYE_007_001 +ICSLA_EYE_086_001 +ICSLA_EYE_026_001 +ICSLA_EYE_008_001 +ICSLA_EYE_016_001 +ICSLA_EYE_080_001 +ICSLA_EYE_082_001 +ICSLA_EYE_024_001 +ICSLA_EYE_081_001 +ICSLA_EYE_025_001 +ICSLA_EYE_023_001 +ICSLA_EYE_004_001 +ICSLA_EYE_011_001 +NINGLA_EYE_081_001 +NINGLA_EYE_014_001 +NINGLA_EYE_024_001 +NINGLA_EYE_085_001 +NINGLA_EYE_025_001 +NINGLA_EYE_017_001 +NINGLA_EYE_010_001 +NINGLA_EYE_027_001 +NINGLA_EYE_002_001 +NINGLA_EYE_008_001 +NINGLA_EYE_009_001 +NINGLA_EYE_016_001 +NINGLA_EYE_082_001 +NINGLA_EYE_086_001 +NINGLA_EYE_006_001 +NINGLA_EYE_022_001 +NINGLA_EYE_004_001 +NINGLA_EYE_020_001 +NINGLA_EYE_011_001 +NINGLA_EYE_019_001 +NINGLA_EYE_083_001 +NINGLA_EYE_080_001 +NINGLA_EYE_018_001 +NINGLA_EYE_026_001 +NINGLA_EYE_012_001 +NINGLA_EYE_003_001 +NINGLA_EYE_084_001 +NINGLA_EYE_013_001 +NINGLA_EYE_005_001 +NINGLA_EYE_023_001 +NINGLA_EYE_021_001 +NINGLA_EYE_007_001 +NINGLA_EYE_015_001 +KMPCLA_EYE_013_001 +KMPCLA_EYE_083_001 +KMPCLA_EYE_025_001 +KMPCLA_EYE_002_001 +KMPCLA_EYE_005_001 +KMPCLA_EYE_008_001 +KMPCLA_EYE_084_001 +KMPCLA_EYE_018_001 +KMPCLA_EYE_024_001 +KMPCLA_EYE_010_001 +KMPCLA_EYE_017_001 +KMPCLA_EYE_011_001 +KMPCLA_EYE_020_001 +KMPCLA_EYE_085_001 +KMPCLA_EYE_015_001 +KMPCLA_EYE_003_001 +KMPCLA_EYE_026_001 +KMPCLA_EYE_004_001 +KMPCLA_EYE_027_001 +KMPCLA_EYE_021_001 +KMPCLA_EYE_014_001 +KMPCLA_EYE_081_001 +KMPCLA_EYE_019_001 +KMPCLA_EYE_080_001 +KMPCLA_EYE_016_001 +KMPCLA_EYE_012_001 +KMPCLA_EYE_006_001 +KMPCLA_EYE_022_001 +KMPCLA_EYE_023_001 +KMPCLA_EYE_086_001 +KMPCLA_EYE_009_001 +KMPCLA_EYE_082_001 +KMPCLA_EYE_007_001 +TCPLA_EYE_002_001 +TCPLA_EYE_003_001 +TCPLA_EYE_004_001 +TCPLA_EYE_005_001 +TCPLA_EYE_006_001 +TCPLA_EYE_007_001 +TCPLA_EYE_008_001 +TCPLA_EYE_009_001 +TCPLA_EYE_010_001 +TCPLA_EYE_011_001 +TCPLA_EYE_012_001 +TCPLA_EYE_013_001 +TCPLA_EYE_014_001 +TCPLA_EYE_015_001 +TCPLA_EYE_016_001 +TCPLA_EYE_017_001 +TCPLA_EYE_018_001 +TCPLA_EYE_019_001 +TCPLA_EYE_023_001 +TCPLA_EYE_024_001 +TCPLA_EYE_025_001 +TCPLA_EYE_026_001 +TCPLA_EYE_027_001 +TCPLA_EYE_080_001 +TCPLA_EYE_081_001 +TCPLA_EYE_082_001 +TCPLA_EYE_083_001 +TCPLA_EYE_084_001 +TCPLA_EYE_085_001 +TCPLA_EYE_086_001 +UCDLA_EYE_002_001 +UCDLA_EYE_003_001 +UCDLA_EYE_004_001 +UCDLA_EYE_005_001 +UCDLA_EYE_006_001 +UCDLA_EYE_007_001 +UCDLA_EYE_008_001 +UCDLA_EYE_009_001 +UCDLA_EYE_010_001 +UCDLA_EYE_011_001 +UCDLA_EYE_012_001 +UCDLA_EYE_013_001 +UCDLA_EYE_014_001 +UCDLA_EYE_015_001 +UCDLA_EYE_016_001 +UCDLA_EYE_017_001 +UCDLA_EYE_018_001 +UCDLA_EYE_019_001 +UCDLA_EYE_023_001 +UCDLA_EYE_024_001 +UCDLA_EYE_025_001 +UCDLA_EYE_026_001 +UCDLA_EYE_027_001 +UCDLA_EYE_080_001 +UCDLA_EYE_081_001 +UCDLA_EYE_082_001 +UCDLA_EYE_083_001 +UCDLA_EYE_084_001 +UCDLA_EYE_085_001 +UCDLA_EYE_086_001 +ICSLA_EYE_002_001 +ICSLA_EYE_003_001 +ICSLA_EYE_004_001 +ICSLA_EYE_005_001 +ICSLA_EYE_006_001 +ICSLA_EYE_007_001 +ICSLA_EYE_008_001 +ICSLA_EYE_009_001 +ICSLA_EYE_010_001 +ICSLA_EYE_011_001 +ICSLA_EYE_012_001 +ICSLA_EYE_013_001 +ICSLA_EYE_014_001 +ICSLA_EYE_015_001 +ICSLA_EYE_016_001 +ICSLA_EYE_017_001 +ICSLA_EYE_018_001 +ICSLA_EYE_019_001 +ICSLA_EYE_023_001 +ICSLA_EYE_024_001 +ICSLA_EYE_025_001 +ICSLA_EYE_026_001 +ICSLA_EYE_027_001 +ICSLA_EYE_080_001 +ICSLA_EYE_081_001 +ICSLA_EYE_082_001 +ICSLA_EYE_083_001 +ICSLA_EYE_084_001 +ICSLA_EYE_085_001 +ICSLA_EYE_086_001 +KMPCLA_EYE_002_001 +KMPCLA_EYE_003_001 +KMPCLA_EYE_004_001 +KMPCLA_EYE_005_001 +KMPCLA_EYE_006_001 +KMPCLA_EYE_007_001 +KMPCLA_EYE_008_001 +KMPCLA_EYE_009_001 +KMPCLA_EYE_010_001 +KMPCLA_EYE_011_001 +KMPCLA_EYE_012_001 +KMPCLA_EYE_013_001 +KMPCLA_EYE_014_001 +KMPCLA_EYE_015_001 +KMPCLA_EYE_016_001 +KMPCLA_EYE_017_001 +KMPCLA_EYE_018_001 +KMPCLA_EYE_019_001 +KMPCLA_EYE_023_001 +KMPCLA_EYE_024_001 +KMPCLA_EYE_025_001 +KMPCLA_EYE_026_001 +KMPCLA_EYE_027_001 +KMPCLA_EYE_080_001 +KMPCLA_EYE_081_001 +KMPCLA_EYE_082_001 +KMPCLA_EYE_083_001 +KMPCLA_EYE_084_001 +KMPCLA_EYE_085_001 +KMPCLA_EYE_086_001 From edfb83ca5c954552d5524ec2bbdc51df64b67d88 Mon Sep 17 00:00:00 2001 From: Marina Kan <113850522+marinak-ebi@users.noreply.github.com> Date: Fri, 24 May 2024 14:23:14 +0100 Subject: [PATCH 3/6] Update CategoryRemapping.tsv for new EYE parameters (copy 1) --- .../extdata/annotation/CategoryRemapping.tsv | 1180 +++++++++++++++++ 1 file changed, 1180 insertions(+) diff --git a/Late adults stats pipeline/DRrequiredAgeing/DRrequiredAgeingPackage/inst/extdata/annotation/CategoryRemapping.tsv b/Late adults stats pipeline/DRrequiredAgeing/DRrequiredAgeingPackage/inst/extdata/annotation/CategoryRemapping.tsv index 93fb7823..71b42233 100644 --- a/Late adults stats pipeline/DRrequiredAgeing/DRrequiredAgeingPackage/inst/extdata/annotation/CategoryRemapping.tsv +++ b/Late adults stats pipeline/DRrequiredAgeing/DRrequiredAgeingPackage/inst/extdata/annotation/CategoryRemapping.tsv @@ -2703,3 +2703,1183 @@ MGP_CSD_116_001 As expected 0 MGP_CSD_116_001 Curved 1 MGP_CSD_116_001 Kinked 1 MGP_CSD_116_001 Other abnormal tail morphology 1 +RBRCLA_EYE_002_001 absent 0 +RBRCLA_EYE_002_001 present right eye 1 +RBRCLA_EYE_002_001 present left eye 1 +RBRCLA_EYE_002_001 present both eyes 1 +RBRCLA_EYE_003_001 absent 0 +RBRCLA_EYE_003_001 present right eye 1 +RBRCLA_EYE_003_001 present left eye 1 +RBRCLA_EYE_003_001 present both eyes 1 +RBRCLA_EYE_004_001 both eyes abnormal 1 +RBRCLA_EYE_004_001 left eye abnormal 1 +RBRCLA_EYE_004_001 right eye abnormal 1 +RBRCLA_EYE_004_001 normal 0 +RBRCLA_EYE_005_001 both eyes closed 1 +RBRCLA_EYE_005_001 left eye closed 1 +RBRCLA_EYE_005_001 right eye closed 1 +RBRCLA_EYE_005_001 normal 0 +RBRCLA_EYE_006_001 both eyes abnormal 1 +RBRCLA_EYE_006_001 left eye abnormal 1 +RBRCLA_EYE_006_001 right eye abnormal 1 +RBRCLA_EYE_006_001 normal 0 +RBRCLA_EYE_007_001 both eyes abnormal 1 +RBRCLA_EYE_007_001 left eye abnormal 1 +RBRCLA_EYE_007_001 right eye abnormal 1 +RBRCLA_EYE_007_001 normal 0 +RBRCLA_EYE_008_001 absent 0 +RBRCLA_EYE_008_001 present right eye 1 +RBRCLA_EYE_008_001 present left eye 1 +RBRCLA_EYE_008_001 present both eyes 1 +RBRCLA_EYE_009_001 absent 0 +RBRCLA_EYE_009_001 present right eye 1 +RBRCLA_EYE_009_001 present left eye 1 +RBRCLA_EYE_009_001 present both eyes 1 +RBRCLA_EYE_010_001 both eyes abnormal 1 +RBRCLA_EYE_010_001 left eye abnormal 1 +RBRCLA_EYE_010_001 right eye abnormal 1 +RBRCLA_EYE_010_001 normal 0 +RBRCLA_EYE_011_001 both eyes abnormal 1 +RBRCLA_EYE_011_001 left eye abnormal 1 +RBRCLA_EYE_011_001 right eye abnormal 1 +RBRCLA_EYE_011_001 normal 0 +RBRCLA_EYE_012_001 both eyes abnormal 1 +RBRCLA_EYE_012_001 left eye abnormal 1 +RBRCLA_EYE_012_001 right eye abnormal 1 +RBRCLA_EYE_012_001 normal 0 +RBRCLA_EYE_013_001 both eyes dilated 1 +RBRCLA_EYE_013_001 left eye dilated 1 +RBRCLA_EYE_013_001 right eye dilated 1 +RBRCLA_EYE_013_001 normal 0 +RBRCLA_EYE_014_001 both eyes abnormal 1 +RBRCLA_EYE_014_001 left eye abnormal 1 +RBRCLA_EYE_014_001 right eye abnormal 1 +RBRCLA_EYE_014_001 normal 0 +RBRCLA_EYE_015_001 both eyes abnormal 1 +RBRCLA_EYE_015_001 left eye abnormal 1 +RBRCLA_EYE_015_001 right eye abnormal 1 +RBRCLA_EYE_015_001 normal 0 +RBRCLA_EYE_016_001 both eyes abnormal 1 +RBRCLA_EYE_016_001 left eye abnormal 1 +RBRCLA_EYE_016_001 right eye abnormal 1 +RBRCLA_EYE_016_001 normal 0 +RBRCLA_EYE_017_001 absent 0 +RBRCLA_EYE_017_001 present right eye 1 +RBRCLA_EYE_017_001 present left eye 1 +RBRCLA_EYE_017_001 present both eyes 1 +RBRCLA_EYE_018_001 absent 0 +RBRCLA_EYE_018_001 present right eye 1 +RBRCLA_EYE_018_001 present left eye 1 +RBRCLA_EYE_018_001 present both eyes 1 +RBRCLA_EYE_019_001 absent 0 +RBRCLA_EYE_019_001 present right eye 1 +RBRCLA_EYE_019_001 present left eye 1 +RBRCLA_EYE_019_001 present both eyes 1 +RBRCLA_EYE_020_001 both eyes abnormal 1 +RBRCLA_EYE_020_001 left eye abnormal 1 +RBRCLA_EYE_020_001 right eye abnormal 1 +RBRCLA_EYE_020_001 normal 0 +RBRCLA_EYE_021_001 both eyes abnormal 1 +RBRCLA_EYE_021_001 left eye abnormal 1 +RBRCLA_EYE_021_001 right eye abnormal 1 +RBRCLA_EYE_021_001 normal 0 +RBRCLA_EYE_022_001 both eyes abnormal 1 +RBRCLA_EYE_022_001 left eye abnormal 1 +RBRCLA_EYE_022_001 right eye abnormal 1 +RBRCLA_EYE_022_001 normal 0 +RBRCLA_EYE_023_001 both eyes abnormal 1 +RBRCLA_EYE_023_001 left eye abnormal 1 +RBRCLA_EYE_023_001 right eye abnormal 1 +RBRCLA_EYE_023_001 normal 0 +RBRCLA_EYE_024_001 both eyes abnormal 1 +RBRCLA_EYE_024_001 left eye abnormal 1 +RBRCLA_EYE_024_001 right eye abnormal 1 +RBRCLA_EYE_024_001 normal 0 +RBRCLA_EYE_025_001 both eyes abnormal 1 +RBRCLA_EYE_025_001 left eye abnormal 1 +RBRCLA_EYE_025_001 right eye abnormal 1 +RBRCLA_EYE_025_001 normal 0 +RBRCLA_EYE_026_001 both eyes abnormal 1 +RBRCLA_EYE_026_001 left eye abnormal 1 +RBRCLA_EYE_026_001 right eye abnormal 1 +RBRCLA_EYE_026_001 normal 0 +RBRCLA_EYE_027_001 absent 0 +RBRCLA_EYE_027_001 present right eye 1 +RBRCLA_EYE_027_001 present left eye 1 +RBRCLA_EYE_027_001 present both eyes 1 +RBRCLA_EYE_080_001 absent 0 +RBRCLA_EYE_080_001 present right eye 1 +RBRCLA_EYE_080_001 present left eye 1 +RBRCLA_EYE_080_001 present both eyes 1 +RBRCLA_EYE_081_001 absent 0 +RBRCLA_EYE_081_001 present right eye 1 +RBRCLA_EYE_081_001 present left eye 1 +RBRCLA_EYE_081_001 present both eyes 1 +RBRCLA_EYE_082_001 both eyes abnormal 1 +RBRCLA_EYE_082_001 left eye abnormal 1 +RBRCLA_EYE_082_001 right eye abnormal 1 +RBRCLA_EYE_082_001 normal 0 +RBRCLA_EYE_083_001 both eyes abnormal 1 +RBRCLA_EYE_083_001 left eye abnormal 1 +RBRCLA_EYE_083_001 right eye abnormal 1 +RBRCLA_EYE_083_001 normal 0 +RBRCLA_EYE_084_001 absent 0 +RBRCLA_EYE_084_001 present right eye 1 +RBRCLA_EYE_084_001 present left eye 1 +RBRCLA_EYE_084_001 present both eyes 1 +RBRCLA_EYE_085_001 absent 0 +RBRCLA_EYE_085_001 present right eye 1 +RBRCLA_EYE_085_001 present left eye 1 +RBRCLA_EYE_085_001 present both eyes 1 +RBRCLA_EYE_086_001 absent 0 +RBRCLA_EYE_086_001 present right eye 1 +RBRCLA_EYE_086_001 present left eye 1 +RBRCLA_EYE_086_001 present both eyes 1 +TCPLA_EYE_080_001 absent 0 +TCPLA_EYE_080_001 present right eye 1 +TCPLA_EYE_080_001 present left eye 1 +TCPLA_EYE_080_001 present both eyes 1 +TCPLA_EYE_085_001 absent 0 +TCPLA_EYE_085_001 present right eye 1 +TCPLA_EYE_085_001 present left eye 1 +TCPLA_EYE_085_001 present both eyes 1 +TCPLA_EYE_010_001 both eyes abnormal 1 +TCPLA_EYE_010_001 left eye abnormal 1 +TCPLA_EYE_010_001 right eye abnormal 1 +TCPLA_EYE_010_001 normal 0 +TCPLA_EYE_082_001 both eyes abnormal 1 +TCPLA_EYE_082_001 left eye abnormal 1 +TCPLA_EYE_082_001 right eye abnormal 1 +TCPLA_EYE_082_001 normal 0 +TCPLA_EYE_019_001 absent 0 +TCPLA_EYE_019_001 present right eye 1 +TCPLA_EYE_019_001 present left eye 1 +TCPLA_EYE_019_001 present both eyes 1 +TCPLA_EYE_014_001 both eyes abnormal 1 +TCPLA_EYE_014_001 left eye abnormal 1 +TCPLA_EYE_014_001 right eye abnormal 1 +TCPLA_EYE_014_001 normal 0 +TCPLA_EYE_081_001 absent 0 +TCPLA_EYE_081_001 present right eye 1 +TCPLA_EYE_081_001 present left eye 1 +TCPLA_EYE_081_001 present both eyes 1 +TCPLA_EYE_025_001 both eyes abnormal 1 +TCPLA_EYE_025_001 left eye abnormal 1 +TCPLA_EYE_025_001 right eye abnormal 1 +TCPLA_EYE_025_001 normal 0 +TCPLA_EYE_002_001 absent 0 +TCPLA_EYE_002_001 present right eye 1 +TCPLA_EYE_002_001 present left eye 1 +TCPLA_EYE_002_001 present both eyes 1 +TCPLA_EYE_018_001 absent 0 +TCPLA_EYE_018_001 present right eye 1 +TCPLA_EYE_018_001 present left eye 1 +TCPLA_EYE_018_001 present both eyes 1 +TCPLA_EYE_011_001 both eyes abnormal 1 +TCPLA_EYE_011_001 left eye abnormal 1 +TCPLA_EYE_011_001 right eye abnormal 1 +TCPLA_EYE_011_001 normal 0 +TCPLA_EYE_016_001 both eyes abnormal 1 +TCPLA_EYE_016_001 left eye abnormal 1 +TCPLA_EYE_016_001 right eye abnormal 1 +TCPLA_EYE_016_001 normal 0 +TCPLA_EYE_005_001 both eyes closed 1 +TCPLA_EYE_005_001 left eye closed 1 +TCPLA_EYE_005_001 right eye closed 1 +TCPLA_EYE_005_001 normal 0 +TCPLA_EYE_017_001 absent 0 +TCPLA_EYE_017_001 present right eye 1 +TCPLA_EYE_017_001 present left eye 1 +TCPLA_EYE_017_001 present both eyes 1 +TCPLA_EYE_083_001 both eyes abnormal 1 +TCPLA_EYE_083_001 left eye abnormal 1 +TCPLA_EYE_083_001 right eye abnormal 1 +TCPLA_EYE_083_001 normal 0 +TCPLA_EYE_084_001 absent 0 +TCPLA_EYE_084_001 present right eye 1 +TCPLA_EYE_084_001 present left eye 1 +TCPLA_EYE_084_001 present both eyes 1 +TCPLA_EYE_026_001 both eyes abnormal 1 +TCPLA_EYE_026_001 left eye abnormal 1 +TCPLA_EYE_026_001 right eye abnormal 1 +TCPLA_EYE_026_001 normal 0 +TCPLA_EYE_027_001 absent 0 +TCPLA_EYE_027_001 present right eye 1 +TCPLA_EYE_027_001 present left eye 1 +TCPLA_EYE_027_001 present both eyes 1 +TCPLA_EYE_023_001 both eyes abnormal 1 +TCPLA_EYE_023_001 left eye abnormal 1 +TCPLA_EYE_023_001 right eye abnormal 1 +TCPLA_EYE_023_001 normal 0 +TCPLA_EYE_024_001 both eyes abnormal 1 +TCPLA_EYE_024_001 left eye abnormal 1 +TCPLA_EYE_024_001 right eye abnormal 1 +TCPLA_EYE_024_001 normal 0 +TCPLA_EYE_004_001 both eyes abnormal 1 +TCPLA_EYE_004_001 left eye abnormal 1 +TCPLA_EYE_004_001 right eye abnormal 1 +TCPLA_EYE_004_001 normal 0 +TCPLA_EYE_007_001 both eyes abnormal 1 +TCPLA_EYE_007_001 left eye abnormal 1 +TCPLA_EYE_007_001 right eye abnormal 1 +TCPLA_EYE_007_001 normal 0 +TCPLA_EYE_015_001 both eyes abnormal 1 +TCPLA_EYE_015_001 left eye abnormal 1 +TCPLA_EYE_015_001 right eye abnormal 1 +TCPLA_EYE_015_001 normal 0 +TCPLA_EYE_013_001 both eyes dilated 1 +TCPLA_EYE_013_001 left eye dilated 1 +TCPLA_EYE_013_001 right eye dilated 1 +TCPLA_EYE_013_001 normal 0 +TCPLA_EYE_008_001 absent 0 +TCPLA_EYE_008_001 present right eye 1 +TCPLA_EYE_008_001 present left eye 1 +TCPLA_EYE_008_001 present both eyes 1 +TCPLA_EYE_006_001 both eyes abnormal 1 +TCPLA_EYE_006_001 left eye abnormal 1 +TCPLA_EYE_006_001 right eye abnormal 1 +TCPLA_EYE_006_001 normal 0 +TCPLA_EYE_086_001 absent 0 +TCPLA_EYE_086_001 present right eye 1 +TCPLA_EYE_086_001 present left eye 1 +TCPLA_EYE_086_001 present both eyes 1 +TCPLA_EYE_009_001 absent 0 +TCPLA_EYE_009_001 present right eye 1 +TCPLA_EYE_009_001 present left eye 1 +TCPLA_EYE_009_001 present both eyes 1 +TCPLA_EYE_012_001 both eyes abnormal 1 +TCPLA_EYE_012_001 left eye abnormal 1 +TCPLA_EYE_012_001 right eye abnormal 1 +TCPLA_EYE_012_001 normal 0 +TCPLA_EYE_003_001 absent 0 +TCPLA_EYE_003_001 present right eye 1 +TCPLA_EYE_003_001 present left eye 1 +TCPLA_EYE_003_001 present both eyes 1 +UCDLA_EYE_011_001 both eyes abnormal 1 +UCDLA_EYE_011_001 left eye abnormal 1 +UCDLA_EYE_011_001 right eye abnormal 1 +UCDLA_EYE_011_001 normal 0 +UCDLA_EYE_082_001 both eyes abnormal 1 +UCDLA_EYE_082_001 left eye abnormal 1 +UCDLA_EYE_082_001 right eye abnormal 1 +UCDLA_EYE_082_001 normal 0 +UCDLA_EYE_083_001 both eyes abnormal 1 +UCDLA_EYE_083_001 left eye abnormal 1 +UCDLA_EYE_083_001 right eye abnormal 1 +UCDLA_EYE_083_001 normal 0 +UCDLA_EYE_002_001 absent 0 +UCDLA_EYE_002_001 present right eye 1 +UCDLA_EYE_002_001 present left eye 1 +UCDLA_EYE_002_001 present both eyes 1 +UCDLA_EYE_084_001 absent 0 +UCDLA_EYE_084_001 present right eye 1 +UCDLA_EYE_084_001 present left eye 1 +UCDLA_EYE_084_001 present both eyes 1 +UCDLA_EYE_023_001 both eyes abnormal 1 +UCDLA_EYE_023_001 left eye abnormal 1 +UCDLA_EYE_023_001 right eye abnormal 1 +UCDLA_EYE_023_001 normal 0 +UCDLA_EYE_015_001 both eyes abnormal 1 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eyes 1 +KMPCLA_EYE_026_001 both eyes abnormal 1 +KMPCLA_EYE_026_001 left eye abnormal 1 +KMPCLA_EYE_026_001 right eye abnormal 1 +KMPCLA_EYE_026_001 normal 0 +KMPCLA_EYE_004_001 both eyes abnormal 1 +KMPCLA_EYE_004_001 left eye abnormal 1 +KMPCLA_EYE_004_001 right eye abnormal 1 +KMPCLA_EYE_004_001 normal 0 +KMPCLA_EYE_027_001 absent 0 +KMPCLA_EYE_027_001 present right eye 1 +KMPCLA_EYE_027_001 present left eye 1 +KMPCLA_EYE_027_001 present both eyes 1 +KMPCLA_EYE_021_001 both eyes abnormal 1 +KMPCLA_EYE_021_001 left eye abnormal 1 +KMPCLA_EYE_021_001 right eye abnormal 1 +KMPCLA_EYE_021_001 normal 0 +KMPCLA_EYE_014_001 both eyes abnormal 1 +KMPCLA_EYE_014_001 left eye abnormal 1 +KMPCLA_EYE_014_001 right eye abnormal 1 +KMPCLA_EYE_014_001 normal 0 +KMPCLA_EYE_081_001 absent 0 +KMPCLA_EYE_081_001 present right eye 1 +KMPCLA_EYE_081_001 present left eye 1 +KMPCLA_EYE_081_001 present both eyes 1 +KMPCLA_EYE_019_001 absent 0 +KMPCLA_EYE_019_001 present right eye 1 +KMPCLA_EYE_019_001 present left eye 1 +KMPCLA_EYE_019_001 present both eyes 1 +KMPCLA_EYE_080_001 absent 0 +KMPCLA_EYE_080_001 present right eye 1 +KMPCLA_EYE_080_001 present left eye 1 +KMPCLA_EYE_080_001 present both eyes 1 +KMPCLA_EYE_016_001 both eyes abnormal 1 +KMPCLA_EYE_016_001 left eye abnormal 1 +KMPCLA_EYE_016_001 right eye abnormal 1 +KMPCLA_EYE_016_001 normal 0 +KMPCLA_EYE_012_001 both eyes abnormal 1 +KMPCLA_EYE_012_001 left eye abnormal 1 +KMPCLA_EYE_012_001 right eye abnormal 1 +KMPCLA_EYE_012_001 normal 0 +KMPCLA_EYE_006_001 both eyes abnormal 1 +KMPCLA_EYE_006_001 left eye abnormal 1 +KMPCLA_EYE_006_001 right eye abnormal 1 +KMPCLA_EYE_006_001 normal 0 +KMPCLA_EYE_022_001 both eyes abnormal 1 +KMPCLA_EYE_022_001 left eye abnormal 1 +KMPCLA_EYE_022_001 right eye abnormal 1 +KMPCLA_EYE_022_001 normal 0 +KMPCLA_EYE_023_001 both eyes abnormal 1 +KMPCLA_EYE_023_001 left eye abnormal 1 +KMPCLA_EYE_023_001 right eye abnormal 1 +KMPCLA_EYE_023_001 normal 0 +KMPCLA_EYE_086_001 absent 0 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+HRWLLA_EYE_081_001 present left eye 1 +HRWLLA_EYE_081_001 present both eyes 1 +HRWLLA_EYE_022_001 both eyes abnormal 1 +HRWLLA_EYE_022_001 left eye abnormal 1 +HRWLLA_EYE_022_001 right eye abnormal 1 +HRWLLA_EYE_022_001 normal 0 +HRWLLA_EYE_004_001 both eyes abnormal 1 +HRWLLA_EYE_004_001 left eye abnormal 1 +HRWLLA_EYE_004_001 right eye abnormal 1 +HRWLLA_EYE_004_001 normal 0 +HRWLLA_EYE_019_001 absent 0 +HRWLLA_EYE_019_001 present right eye 1 +HRWLLA_EYE_019_001 present left eye 1 +HRWLLA_EYE_019_001 present both eyes 1 +HRWLLA_EYE_020_001 both eyes abnormal 1 +HRWLLA_EYE_020_001 left eye abnormal 1 +HRWLLA_EYE_020_001 right eye abnormal 1 +HRWLLA_EYE_020_001 normal 0 +HRWLLA_EYE_085_001 absent 0 +HRWLLA_EYE_085_001 present right eye 1 +HRWLLA_EYE_085_001 present left eye 1 +HRWLLA_EYE_085_001 present both eyes 1 +HRWLLA_EYE_018_001 absent 0 +HRWLLA_EYE_018_001 present right eye 1 +HRWLLA_EYE_018_001 present left eye 1 +HRWLLA_EYE_018_001 present both eyes 1 +HRWLLA_EYE_005_001 both eyes closed 1 +HRWLLA_EYE_005_001 left eye closed 1 +HRWLLA_EYE_005_001 right eye closed 1 +HRWLLA_EYE_005_001 normal 0 +HRWLLA_EYE_027_001 absent 0 +HRWLLA_EYE_027_001 present right eye 1 +HRWLLA_EYE_027_001 present left eye 1 +HRWLLA_EYE_027_001 present both eyes 1 +HRWLLA_EYE_021_001 both eyes abnormal 1 +HRWLLA_EYE_021_001 left eye abnormal 1 +HRWLLA_EYE_021_001 right eye abnormal 1 +HRWLLA_EYE_021_001 normal 0 +HRWLLA_EYE_080_001 absent 0 +HRWLLA_EYE_080_001 present right eye 1 +HRWLLA_EYE_080_001 present left eye 1 +HRWLLA_EYE_080_001 present both eyes 1 +HRWLLA_EYE_023_001 both eyes abnormal 1 +HRWLLA_EYE_023_001 left eye abnormal 1 +HRWLLA_EYE_023_001 right eye abnormal 1 +HRWLLA_EYE_023_001 normal 0 +HRWLLA_EYE_017_001 absent 0 +HRWLLA_EYE_017_001 present right eye 1 +HRWLLA_EYE_017_001 present left eye 1 +HRWLLA_EYE_017_001 present both eyes 1 +HRWLLA_EYE_011_001 both eyes abnormal 1 +HRWLLA_EYE_011_001 left eye abnormal 1 +HRWLLA_EYE_011_001 right eye abnormal 1 +HRWLLA_EYE_011_001 normal 0 +HRWLLA_EYE_013_001 both eyes dilated 1 +HRWLLA_EYE_013_001 left eye dilated 1 +HRWLLA_EYE_013_001 right eye dilated 1 +HRWLLA_EYE_013_001 normal 0 +HRWLLA_EYE_003_001 absent 0 +HRWLLA_EYE_003_001 present right eye 1 +HRWLLA_EYE_003_001 present left eye 1 +HRWLLA_EYE_003_001 present both eyes 1 +HRWLLA_EYE_086_001 absent 0 +HRWLLA_EYE_086_001 present right eye 1 +HRWLLA_EYE_086_001 present left eye 1 +HRWLLA_EYE_086_001 present both eyes 1 +HRWLLA_EYE_083_001 both eyes abnormal 1 +HRWLLA_EYE_083_001 left eye abnormal 1 +HRWLLA_EYE_083_001 right eye abnormal 1 +HRWLLA_EYE_083_001 normal 0 +HRWLLA_EYE_009_001 absent 0 +HRWLLA_EYE_009_001 present right eye 1 +HRWLLA_EYE_009_001 present left eye 1 +HRWLLA_EYE_009_001 present both eyes 1 +HRWLLA_EYE_002_001 absent 0 +HRWLLA_EYE_002_001 present right eye 1 +HRWLLA_EYE_002_001 present left eye 1 +HRWLLA_EYE_002_001 present both eyes 1 +HRWLLA_EYE_012_001 both eyes abnormal 1 +HRWLLA_EYE_012_001 left eye abnormal 1 +HRWLLA_EYE_012_001 right eye abnormal 1 +HRWLLA_EYE_012_001 normal 0 +HRWLLA_EYE_015_001 both eyes abnormal 1 +HRWLLA_EYE_015_001 left eye abnormal 1 +HRWLLA_EYE_015_001 right eye abnormal 1 +HRWLLA_EYE_015_001 normal 0 +HRWLLA_EYE_025_001 both eyes abnormal 1 +HRWLLA_EYE_025_001 left eye abnormal 1 +HRWLLA_EYE_025_001 right eye abnormal 1 +HRWLLA_EYE_025_001 normal 0 +HRWLLA_EYE_007_001 both eyes abnormal 1 +HRWLLA_EYE_007_001 left eye abnormal 1 +HRWLLA_EYE_007_001 right eye abnormal 1 +HRWLLA_EYE_007_001 normal 0 +JAXLA_EYE_086_001 absent 0 +JAXLA_EYE_086_001 present right eye 1 +JAXLA_EYE_086_001 present left eye 1 +JAXLA_EYE_086_001 present both eyes 1 +JAXLA_EYE_009_001 absent 0 +JAXLA_EYE_009_001 present right eye 1 +JAXLA_EYE_009_001 present left eye 1 +JAXLA_EYE_009_001 present both eyes 1 +JAXLA_EYE_006_001 both eyes abnormal 1 +JAXLA_EYE_006_001 left eye abnormal 1 +JAXLA_EYE_006_001 right eye abnormal 1 +JAXLA_EYE_006_001 normal 0 +JAXLA_EYE_002_001 absent 0 +JAXLA_EYE_002_001 present right eye 1 +JAXLA_EYE_002_001 present left eye 1 +JAXLA_EYE_002_001 present both eyes 1 +JAXLA_EYE_083_001 both eyes abnormal 1 +JAXLA_EYE_083_001 left eye abnormal 1 +JAXLA_EYE_083_001 right eye abnormal 1 +JAXLA_EYE_083_001 normal 0 +JAXLA_EYE_023_001 both eyes abnormal 1 +JAXLA_EYE_023_001 left eye abnormal 1 +JAXLA_EYE_023_001 right eye abnormal 1 +JAXLA_EYE_023_001 normal 0 +JAXLA_EYE_027_001 absent 0 +JAXLA_EYE_027_001 present right eye 1 +JAXLA_EYE_027_001 present left eye 1 +JAXLA_EYE_027_001 present both eyes 1 +JAXLA_EYE_016_001 both eyes abnormal 1 +JAXLA_EYE_016_001 left eye abnormal 1 +JAXLA_EYE_016_001 right eye abnormal 1 +JAXLA_EYE_016_001 normal 0 +JAXLA_EYE_018_001 absent 0 +JAXLA_EYE_018_001 present right eye 1 +JAXLA_EYE_018_001 present left eye 1 +JAXLA_EYE_018_001 present both eyes 1 +JAXLA_EYE_024_001 both eyes abnormal 1 +JAXLA_EYE_024_001 left eye abnormal 1 +JAXLA_EYE_024_001 right eye abnormal 1 +JAXLA_EYE_024_001 normal 0 +JAXLA_EYE_015_001 both eyes abnormal 1 +JAXLA_EYE_015_001 left eye abnormal 1 +JAXLA_EYE_015_001 right eye abnormal 1 +JAXLA_EYE_015_001 normal 0 +JAXLA_EYE_021_001 both eyes abnormal 1 +JAXLA_EYE_021_001 left eye abnormal 1 +JAXLA_EYE_021_001 right eye abnormal 1 +JAXLA_EYE_021_001 normal 0 +JAXLA_EYE_082_001 both eyes abnormal 1 +JAXLA_EYE_082_001 left eye abnormal 1 +JAXLA_EYE_082_001 right eye abnormal 1 +JAXLA_EYE_082_001 normal 0 +JAXLA_EYE_005_001 both eyes closed 1 +JAXLA_EYE_005_001 left eye closed 1 +JAXLA_EYE_005_001 right eye closed 1 +JAXLA_EYE_005_001 normal 0 +JAXLA_EYE_026_001 both eyes abnormal 1 +JAXLA_EYE_026_001 left eye abnormal 1 +JAXLA_EYE_026_001 right eye abnormal 1 +JAXLA_EYE_026_001 normal 0 +JAXLA_EYE_080_001 absent 0 +JAXLA_EYE_080_001 present right eye 1 +JAXLA_EYE_080_001 present left eye 1 +JAXLA_EYE_080_001 present both eyes 1 +JAXLA_EYE_008_001 absent 0 +JAXLA_EYE_008_001 present right eye 1 +JAXLA_EYE_008_001 present left eye 1 +JAXLA_EYE_008_001 present both eyes 1 +JAXLA_EYE_011_001 both eyes abnormal 1 +JAXLA_EYE_011_001 left eye abnormal 1 +JAXLA_EYE_011_001 right eye abnormal 1 +JAXLA_EYE_011_001 normal 0 +JAXLA_EYE_084_001 absent 0 +JAXLA_EYE_084_001 present right eye 1 +JAXLA_EYE_084_001 present left eye 1 +JAXLA_EYE_084_001 present both eyes 1 +JAXLA_EYE_085_001 absent 0 +JAXLA_EYE_085_001 present right eye 1 +JAXLA_EYE_085_001 present left eye 1 +JAXLA_EYE_085_001 present both eyes 1 +JAXLA_EYE_010_001 both eyes abnormal 1 +JAXLA_EYE_010_001 left eye abnormal 1 +JAXLA_EYE_010_001 right eye abnormal 1 +JAXLA_EYE_010_001 normal 0 +JAXLA_EYE_003_001 absent 0 +JAXLA_EYE_003_001 present right eye 1 +JAXLA_EYE_003_001 present left eye 1 +JAXLA_EYE_003_001 present both eyes 1 +JAXLA_EYE_007_001 both eyes abnormal 1 +JAXLA_EYE_007_001 left eye abnormal 1 +JAXLA_EYE_007_001 right eye abnormal 1 +JAXLA_EYE_007_001 normal 0 +JAXLA_EYE_025_001 both eyes abnormal 1 +JAXLA_EYE_025_001 left eye abnormal 1 +JAXLA_EYE_025_001 right eye abnormal 1 +JAXLA_EYE_025_001 normal 0 +JAXLA_EYE_012_001 both eyes abnormal 1 +JAXLA_EYE_012_001 left eye abnormal 1 +JAXLA_EYE_012_001 right eye abnormal 1 +JAXLA_EYE_012_001 normal 0 +JAXLA_EYE_014_001 both eyes abnormal 1 +JAXLA_EYE_014_001 left eye abnormal 1 +JAXLA_EYE_014_001 right eye abnormal 1 +JAXLA_EYE_014_001 normal 0 +JAXLA_EYE_020_001 both eyes abnormal 1 +JAXLA_EYE_020_001 left eye abnormal 1 +JAXLA_EYE_020_001 right eye abnormal 1 +JAXLA_EYE_020_001 normal 0 +JAXLA_EYE_022_001 both eyes abnormal 1 +JAXLA_EYE_022_001 left eye abnormal 1 +JAXLA_EYE_022_001 right eye abnormal 1 +JAXLA_EYE_022_001 normal 0 +JAXLA_EYE_017_001 absent 0 +JAXLA_EYE_017_001 present right eye 1 +JAXLA_EYE_017_001 present left eye 1 +JAXLA_EYE_017_001 present both eyes 1 +JAXLA_EYE_013_001 both eyes dilated 1 +JAXLA_EYE_013_001 left eye dilated 1 +JAXLA_EYE_013_001 right eye dilated 1 +JAXLA_EYE_013_001 normal 0 +JAXLA_EYE_019_001 absent 0 +JAXLA_EYE_019_001 present right eye 1 +JAXLA_EYE_019_001 present left eye 1 +JAXLA_EYE_019_001 present both eyes 1 +JAXLA_EYE_081_001 absent 0 +JAXLA_EYE_081_001 present right eye 1 +JAXLA_EYE_081_001 present left eye 1 +JAXLA_EYE_081_001 present both eyes 1 +JAXLA_EYE_004_001 both eyes abnormal 1 +JAXLA_EYE_004_001 left eye abnormal 1 +JAXLA_EYE_004_001 right eye abnormal 1 +JAXLA_EYE_004_001 normal 0 +TCPLA_EYE_092_002 both eyes abnormal 1 +TCPLA_EYE_092_002 left eye abnormal 1 +TCPLA_EYE_092_002 right eye abnormal 1 +TCPLA_EYE_092_002 normal 0 +UCDLA_EYE_092_002 both eyes abnormal 1 +UCDLA_EYE_092_002 left eye abnormal 1 +UCDLA_EYE_092_002 right eye abnormal 1 +UCDLA_EYE_092_002 normal 0 +ICSLA_EYE_092_002 both eyes abnormal 1 +ICSLA_EYE_092_002 left eye abnormal 1 +ICSLA_EYE_092_002 right eye abnormal 1 +ICSLA_EYE_092_002 normal 0 +HRWLLA_EYE_092_002 both eyes abnormal 1 +HRWLLA_EYE_092_002 left eye abnormal 1 +HRWLLA_EYE_092_002 right eye abnormal 1 +HRWLLA_EYE_092_002 normal 0 +JAXLA_EYE_092_002 both eyes abnormal 1 +JAXLA_EYE_092_002 left eye abnormal 1 +JAXLA_EYE_092_002 right eye abnormal 1 +JAXLA_EYE_092_002 normal 0 +BCMLA_EYE_092_002 both eyes abnormal 1 +BCMLA_EYE_092_002 left eye abnormal 1 +BCMLA_EYE_092_002 right eye abnormal 1 +BCMLA_EYE_092_002 normal 0 +KMPCLA_EYE_092_002 both eyes abnormal 1 +KMPCLA_EYE_092_002 left eye abnormal 1 +KMPCLA_EYE_092_002 right eye abnormal 1 +KMPCLA_EYE_092_002 normal 0 From e97e6dc8f456e00c95d79dbb83f08aafed6281e5 Mon Sep 17 00:00:00 2001 From: Marina Kan <113850522+marinak-ebi@users.noreply.github.com> Date: Fri, 24 May 2024 14:23:19 +0100 Subject: [PATCH 4/6] Update CategoryRemapping.tsv for new EYE parameters (copy 2) --- .../jobs/Postgres/CategoryRemapping.tsv | 1180 +++++++++++++++++ 1 file changed, 1180 insertions(+) diff --git a/Late adults stats pipeline/DRrequiredAgeing/DRrequiredAgeingPackage/inst/extdata/StatsPipeline/jobs/Postgres/CategoryRemapping.tsv b/Late adults stats pipeline/DRrequiredAgeing/DRrequiredAgeingPackage/inst/extdata/StatsPipeline/jobs/Postgres/CategoryRemapping.tsv index 93fb7823..71b42233 100644 --- a/Late adults stats pipeline/DRrequiredAgeing/DRrequiredAgeingPackage/inst/extdata/StatsPipeline/jobs/Postgres/CategoryRemapping.tsv +++ b/Late adults stats pipeline/DRrequiredAgeing/DRrequiredAgeingPackage/inst/extdata/StatsPipeline/jobs/Postgres/CategoryRemapping.tsv @@ -2703,3 +2703,1183 @@ MGP_CSD_116_001 As expected 0 MGP_CSD_116_001 Curved 1 MGP_CSD_116_001 Kinked 1 MGP_CSD_116_001 Other abnormal tail morphology 1 +RBRCLA_EYE_002_001 absent 0 +RBRCLA_EYE_002_001 present right eye 1 +RBRCLA_EYE_002_001 present left eye 1 +RBRCLA_EYE_002_001 present both eyes 1 +RBRCLA_EYE_003_001 absent 0 +RBRCLA_EYE_003_001 present right eye 1 +RBRCLA_EYE_003_001 present left eye 1 +RBRCLA_EYE_003_001 present both eyes 1 +RBRCLA_EYE_004_001 both eyes abnormal 1 +RBRCLA_EYE_004_001 left eye abnormal 1 +RBRCLA_EYE_004_001 right eye abnormal 1 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abnormal 1 +RBRCLA_EYE_011_001 right eye abnormal 1 +RBRCLA_EYE_011_001 normal 0 +RBRCLA_EYE_012_001 both eyes abnormal 1 +RBRCLA_EYE_012_001 left eye abnormal 1 +RBRCLA_EYE_012_001 right eye abnormal 1 +RBRCLA_EYE_012_001 normal 0 +RBRCLA_EYE_013_001 both eyes dilated 1 +RBRCLA_EYE_013_001 left eye dilated 1 +RBRCLA_EYE_013_001 right eye dilated 1 +RBRCLA_EYE_013_001 normal 0 +RBRCLA_EYE_014_001 both eyes abnormal 1 +RBRCLA_EYE_014_001 left eye abnormal 1 +RBRCLA_EYE_014_001 right eye abnormal 1 +RBRCLA_EYE_014_001 normal 0 +RBRCLA_EYE_015_001 both eyes abnormal 1 +RBRCLA_EYE_015_001 left eye abnormal 1 +RBRCLA_EYE_015_001 right eye abnormal 1 +RBRCLA_EYE_015_001 normal 0 +RBRCLA_EYE_016_001 both eyes abnormal 1 +RBRCLA_EYE_016_001 left eye abnormal 1 +RBRCLA_EYE_016_001 right eye abnormal 1 +RBRCLA_EYE_016_001 normal 0 +RBRCLA_EYE_017_001 absent 0 +RBRCLA_EYE_017_001 present right eye 1 +RBRCLA_EYE_017_001 present left eye 1 +RBRCLA_EYE_017_001 present both eyes 1 +RBRCLA_EYE_018_001 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+HRWLLA_EYE_015_001 left eye abnormal 1 +HRWLLA_EYE_015_001 right eye abnormal 1 +HRWLLA_EYE_015_001 normal 0 +HRWLLA_EYE_025_001 both eyes abnormal 1 +HRWLLA_EYE_025_001 left eye abnormal 1 +HRWLLA_EYE_025_001 right eye abnormal 1 +HRWLLA_EYE_025_001 normal 0 +HRWLLA_EYE_007_001 both eyes abnormal 1 +HRWLLA_EYE_007_001 left eye abnormal 1 +HRWLLA_EYE_007_001 right eye abnormal 1 +HRWLLA_EYE_007_001 normal 0 +JAXLA_EYE_086_001 absent 0 +JAXLA_EYE_086_001 present right eye 1 +JAXLA_EYE_086_001 present left eye 1 +JAXLA_EYE_086_001 present both eyes 1 +JAXLA_EYE_009_001 absent 0 +JAXLA_EYE_009_001 present right eye 1 +JAXLA_EYE_009_001 present left eye 1 +JAXLA_EYE_009_001 present both eyes 1 +JAXLA_EYE_006_001 both eyes abnormal 1 +JAXLA_EYE_006_001 left eye abnormal 1 +JAXLA_EYE_006_001 right eye abnormal 1 +JAXLA_EYE_006_001 normal 0 +JAXLA_EYE_002_001 absent 0 +JAXLA_EYE_002_001 present right eye 1 +JAXLA_EYE_002_001 present left eye 1 +JAXLA_EYE_002_001 present both eyes 1 +JAXLA_EYE_083_001 both eyes abnormal 1 +JAXLA_EYE_083_001 left eye abnormal 1 +JAXLA_EYE_083_001 right eye abnormal 1 +JAXLA_EYE_083_001 normal 0 +JAXLA_EYE_023_001 both eyes abnormal 1 +JAXLA_EYE_023_001 left eye abnormal 1 +JAXLA_EYE_023_001 right eye abnormal 1 +JAXLA_EYE_023_001 normal 0 +JAXLA_EYE_027_001 absent 0 +JAXLA_EYE_027_001 present right eye 1 +JAXLA_EYE_027_001 present left eye 1 +JAXLA_EYE_027_001 present both eyes 1 +JAXLA_EYE_016_001 both eyes abnormal 1 +JAXLA_EYE_016_001 left eye abnormal 1 +JAXLA_EYE_016_001 right eye abnormal 1 +JAXLA_EYE_016_001 normal 0 +JAXLA_EYE_018_001 absent 0 +JAXLA_EYE_018_001 present right eye 1 +JAXLA_EYE_018_001 present left eye 1 +JAXLA_EYE_018_001 present both eyes 1 +JAXLA_EYE_024_001 both eyes abnormal 1 +JAXLA_EYE_024_001 left eye abnormal 1 +JAXLA_EYE_024_001 right eye abnormal 1 +JAXLA_EYE_024_001 normal 0 +JAXLA_EYE_015_001 both eyes abnormal 1 +JAXLA_EYE_015_001 left eye abnormal 1 +JAXLA_EYE_015_001 right eye abnormal 1 +JAXLA_EYE_015_001 normal 0 +JAXLA_EYE_021_001 both eyes abnormal 1 +JAXLA_EYE_021_001 left eye abnormal 1 +JAXLA_EYE_021_001 right eye abnormal 1 +JAXLA_EYE_021_001 normal 0 +JAXLA_EYE_082_001 both eyes abnormal 1 +JAXLA_EYE_082_001 left eye abnormal 1 +JAXLA_EYE_082_001 right eye abnormal 1 +JAXLA_EYE_082_001 normal 0 +JAXLA_EYE_005_001 both eyes closed 1 +JAXLA_EYE_005_001 left eye closed 1 +JAXLA_EYE_005_001 right eye closed 1 +JAXLA_EYE_005_001 normal 0 +JAXLA_EYE_026_001 both eyes abnormal 1 +JAXLA_EYE_026_001 left eye abnormal 1 +JAXLA_EYE_026_001 right eye abnormal 1 +JAXLA_EYE_026_001 normal 0 +JAXLA_EYE_080_001 absent 0 +JAXLA_EYE_080_001 present right eye 1 +JAXLA_EYE_080_001 present left eye 1 +JAXLA_EYE_080_001 present both eyes 1 +JAXLA_EYE_008_001 absent 0 +JAXLA_EYE_008_001 present right eye 1 +JAXLA_EYE_008_001 present left eye 1 +JAXLA_EYE_008_001 present both eyes 1 +JAXLA_EYE_011_001 both eyes abnormal 1 +JAXLA_EYE_011_001 left eye abnormal 1 +JAXLA_EYE_011_001 right eye abnormal 1 +JAXLA_EYE_011_001 normal 0 +JAXLA_EYE_084_001 absent 0 +JAXLA_EYE_084_001 present right eye 1 +JAXLA_EYE_084_001 present left eye 1 +JAXLA_EYE_084_001 present both eyes 1 +JAXLA_EYE_085_001 absent 0 +JAXLA_EYE_085_001 present right eye 1 +JAXLA_EYE_085_001 present left eye 1 +JAXLA_EYE_085_001 present both eyes 1 +JAXLA_EYE_010_001 both eyes abnormal 1 +JAXLA_EYE_010_001 left eye abnormal 1 +JAXLA_EYE_010_001 right eye abnormal 1 +JAXLA_EYE_010_001 normal 0 +JAXLA_EYE_003_001 absent 0 +JAXLA_EYE_003_001 present right eye 1 +JAXLA_EYE_003_001 present left eye 1 +JAXLA_EYE_003_001 present both eyes 1 +JAXLA_EYE_007_001 both eyes abnormal 1 +JAXLA_EYE_007_001 left eye abnormal 1 +JAXLA_EYE_007_001 right eye abnormal 1 +JAXLA_EYE_007_001 normal 0 +JAXLA_EYE_025_001 both eyes abnormal 1 +JAXLA_EYE_025_001 left eye abnormal 1 +JAXLA_EYE_025_001 right eye abnormal 1 +JAXLA_EYE_025_001 normal 0 +JAXLA_EYE_012_001 both eyes abnormal 1 +JAXLA_EYE_012_001 left eye abnormal 1 +JAXLA_EYE_012_001 right eye abnormal 1 +JAXLA_EYE_012_001 normal 0 +JAXLA_EYE_014_001 both eyes abnormal 1 +JAXLA_EYE_014_001 left eye abnormal 1 +JAXLA_EYE_014_001 right eye abnormal 1 +JAXLA_EYE_014_001 normal 0 +JAXLA_EYE_020_001 both eyes abnormal 1 +JAXLA_EYE_020_001 left eye abnormal 1 +JAXLA_EYE_020_001 right eye abnormal 1 +JAXLA_EYE_020_001 normal 0 +JAXLA_EYE_022_001 both eyes abnormal 1 +JAXLA_EYE_022_001 left eye abnormal 1 +JAXLA_EYE_022_001 right eye abnormal 1 +JAXLA_EYE_022_001 normal 0 +JAXLA_EYE_017_001 absent 0 +JAXLA_EYE_017_001 present right eye 1 +JAXLA_EYE_017_001 present left eye 1 +JAXLA_EYE_017_001 present both eyes 1 +JAXLA_EYE_013_001 both eyes dilated 1 +JAXLA_EYE_013_001 left eye dilated 1 +JAXLA_EYE_013_001 right eye dilated 1 +JAXLA_EYE_013_001 normal 0 +JAXLA_EYE_019_001 absent 0 +JAXLA_EYE_019_001 present right eye 1 +JAXLA_EYE_019_001 present left eye 1 +JAXLA_EYE_019_001 present both eyes 1 +JAXLA_EYE_081_001 absent 0 +JAXLA_EYE_081_001 present right eye 1 +JAXLA_EYE_081_001 present left eye 1 +JAXLA_EYE_081_001 present both eyes 1 +JAXLA_EYE_004_001 both eyes abnormal 1 +JAXLA_EYE_004_001 left eye abnormal 1 +JAXLA_EYE_004_001 right eye abnormal 1 +JAXLA_EYE_004_001 normal 0 +TCPLA_EYE_092_002 both eyes abnormal 1 +TCPLA_EYE_092_002 left eye abnormal 1 +TCPLA_EYE_092_002 right eye abnormal 1 +TCPLA_EYE_092_002 normal 0 +UCDLA_EYE_092_002 both eyes abnormal 1 +UCDLA_EYE_092_002 left eye abnormal 1 +UCDLA_EYE_092_002 right eye abnormal 1 +UCDLA_EYE_092_002 normal 0 +ICSLA_EYE_092_002 both eyes abnormal 1 +ICSLA_EYE_092_002 left eye abnormal 1 +ICSLA_EYE_092_002 right eye abnormal 1 +ICSLA_EYE_092_002 normal 0 +HRWLLA_EYE_092_002 both eyes abnormal 1 +HRWLLA_EYE_092_002 left eye abnormal 1 +HRWLLA_EYE_092_002 right eye abnormal 1 +HRWLLA_EYE_092_002 normal 0 +JAXLA_EYE_092_002 both eyes abnormal 1 +JAXLA_EYE_092_002 left eye abnormal 1 +JAXLA_EYE_092_002 right eye abnormal 1 +JAXLA_EYE_092_002 normal 0 +BCMLA_EYE_092_002 both eyes abnormal 1 +BCMLA_EYE_092_002 left eye abnormal 1 +BCMLA_EYE_092_002 right eye abnormal 1 +BCMLA_EYE_092_002 normal 0 +KMPCLA_EYE_092_002 both eyes abnormal 1 +KMPCLA_EYE_092_002 left eye abnormal 1 +KMPCLA_EYE_092_002 right eye abnormal 1 +KMPCLA_EYE_092_002 normal 0 From 88511de1a30b20540d7e91b89985612974cbe725 Mon Sep 17 00:00:00 2001 From: Marina Kan <113850522+marinak-ebi@users.noreply.github.com> Date: Fri, 24 May 2024 14:26:01 +0100 Subject: [PATCH 5/6] Add eye_patch.py, a temporary module for sync with IMPRESS --- eye_patch.py | 90 ++++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 90 insertions(+) create mode 100644 eye_patch.py diff --git a/eye_patch.py b/eye_patch.py new file mode 100644 index 00000000..0f6d445f --- /dev/null +++ b/eye_patch.py @@ -0,0 +1,90 @@ +"""This is a temporary module to synchronise the parameters/options lists with IMPRESS. +Given the size of the files (CategoryRemapping.tsv, MergeParameterList.txt), it's impossible to modify them byhand, so this module is used instead. +In the future, parameter mapping and representation will be improved and refactored, so this module will no longer be necessary.""" + +import csv + +print("Load CategoryMap.conf") +category_map: dict = dict() +for line in open( + "Late adults stats pipeline/DRrequiredAgeing/DRrequiredAgeingPackage/inst/extdata/CategoryMap.conf" +): + line = line.rstrip() + if ":" in line: + a, b = line.split(":") + category_map[a] = b + +print("Load MergeParameterList.txt") +merge_parameter_list = set( + open( + "Late adults stats pipeline/DRrequiredAgeing/DRrequiredAgeingPackage/inst/extdata/MergeParameterList.txt" + ) + .read() + .splitlines()[1:] +) + +print("Load CategoryRemapping.tsv") +# Center, parameter, value: assignment. +c_p_v_a: dict = {} +with open( + "Late adults stats pipeline/DRrequiredAgeing/DRrequiredAgeingPackage/inst/extdata/annotation/CategoryRemapping.tsv", + mode="r", + newline="", +) as file: + file.readline() + for row in file: + centre_parameter, value, assignment = row.rstrip().split("\t") + if not "_EYE_" in centre_parameter: + continue + parts = centre_parameter.split("_") + centre = parts[0] + parameter = "_".join(parts[1:]) + c_p_v_a[f"{centre}/{parameter}/{value}"] = int(assignment) +# Parameter, value: assignment. +p_v_a: dict = {} +for c_p_v, a in c_p_v_a.items(): + c, p, v = c_p_v.split("/") + key = f"{p}_{v}" + if key in p_v_a: + assert p_v_a[key] == a + else: + p_v_a[key] = a +# Add manual new assignments. +p_v_a["EYE_092_002_normal"] = 0 +p_v_a["EYE_092_002_both eyes abnormal"] = 1 +p_v_a["EYE_092_002_right eye abnormal"] = 1 +p_v_a["EYE_092_002_left eye abnormal"] = 1 + +print("Process the new file") +merge_parameter_list_out = open( + "Late adults stats pipeline/DRrequiredAgeing/DRrequiredAgeingPackage/inst/extdata/MergeParameterList.txt", + "a", +) +category_remapping_out = open( + "Late adults stats pipeline/DRrequiredAgeing/DRrequiredAgeingPackage/inst/extdata/annotation/CategoryRemapping.tsv", + "a", +) +with open("LA_EYE_parameters.csv", mode="r", newline="") as file: + reader = csv.DictReader(file) + for row in reader: + # Extract centre and the actual parameter. + centre_parameter = row["parameter_stable_id"] + parts = centre_parameter.split("_") + centre = parts[0] + parameter = "_".join(parts[1:]) + # Amend MergeParameterList, if needed. + if centre_parameter not in merge_parameter_list: + merge_parameter_list_out.write(centre_parameter + "\n") + # Amend CategoryRemapping.tsv, if needed. + for value in sorted(row["options"].split(";")): + renamed = category_map.get(value, value) + if renamed == "NA": + continue + key = f"{centre}/{parameter}/{renamed}" + if not key in c_p_v_a: + a = p_v_a[f"{parameter}_{renamed}"] + category_remapping_out.write(f"{centre_parameter}\t{renamed}\t{a}\n") + c_p_v_a[key] = a + +merge_parameter_list_out.close() +category_remapping_out.close() From 03ea4a8026bfb7c6f2feee1ca7dde34d639977f6 Mon Sep 17 00:00:00 2001 From: Marina Kan <113850522+marinak-ebi@users.noreply.github.com> Date: Fri, 24 May 2024 14:28:14 +0100 Subject: [PATCH 6/6] Fix typo --- eye_patch.py | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/eye_patch.py b/eye_patch.py index 0f6d445f..376dea41 100644 --- a/eye_patch.py +++ b/eye_patch.py @@ -1,6 +1,7 @@ """This is a temporary module to synchronise the parameters/options lists with IMPRESS. -Given the size of the files (CategoryRemapping.tsv, MergeParameterList.txt), it's impossible to modify them byhand, so this module is used instead. -In the future, parameter mapping and representation will be improved and refactored, so this module will no longer be necessary.""" +Given the size of the files (CategoryRemapping.tsv, MergeParameterList.txt), it's impossible +to modify them by hand, so this module is used instead. In the future, parameter mapping +and representation will be improved and refactored, so this module will no longer be necessary.""" import csv