+
+
+
Get the variables in the Microbiome Dataset by their names.
+The requested variables could belong to any collection or
+to the metadata. The returned data.table will contain the
+requested variables as columns and any appropriate identifiers.
+If one of the requested variables cannot be returned, a warning
+will be printed.
+
+
Usage
+
getVariables(object, variables)
+
+# S4 method for MbioDataset
+getVariables(object, variables)
+
+
Arguments
+
- object
+A Microbiome Dataset
- variables
+The names of the variables to return. This should be a named list
+where the names are collection names and the values are variable names for that collection.
+For the case of metadata variables, the name should be "metadata".
+
Value
+
+
+
a data.table of the requested variables
+
+
Examples
+
getCollectionVariableNames(microbiomeData::DiabImmune, "16S (V4) Genus")
+#> [1] "28-4"
+#> [2] "Abiotrophia"
+#> [3] "Acetanaerobacterium"
+#> [4] "Acetobacter"
+#> [5] "Achromobacter"
+#> [6] "Acidaminococcus"
+#> [7] "Acidibacter"
+#> [8] "Acidiphilium"
+#> [9] "Acidipropionibacterium"
+#> [10] "Acidocella"
+#> [11] "Acidovorax"
+#> [12] "Acinetobacter"
+#> [13] "Actinobacillus"
+#> [14] "Actinobaculum"
+#> [15] "Actinomyces"
+#> [16] "Actinotignum"
+#> [17] "Adlercreutzia"
+#> [18] "Aerococcus"
+#> [19] "Aeromonas"
+#> [20] "Afipia"
+#> [21] "Agathobacter"
+#> [22] "Aggregatibacter"
+#> [23] "Akkermansia"
+#> [24] "Alcaligenes"
+#> [25] "Alicycliphilus"
+#> [26] "Alistipes"
+#> [27] "Allisonella"
+#> [28] "Allobaculum"
+#> [29] "Alloprevotella"
+#> [30] "Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium"
+#> [31] "Alloscardovia"
+#> [32] "Amaricoccus"
+#> [33] "Amnibacterium"
+#> [34] "Anaerobium"
+#> [35] "Anaerocolumna"
+#> [36] "Anaerofilum"
+#> [37] "Anaerofustis"
+#> [38] "Anaeroglobus"
+#> [39] "Anaeromyxobacter"
+#> [40] "Anaeroplasma"
+#> [41] "Anaerosporobacter"
+#> [42] "Anaerosporomusa"
+#> [43] "Anaerostignum"
+#> [44] "Anaerostipes"
+#> [45] "Anaerotruncus"
+#> [46] "Angelakisella"
+#> [47] "Angustibacter"
+#> [48] "Anoxybacillus"
+#> [49] "Aquabacterium"
+#> [50] "Aquamonas"
+#> [51] "Arcanobacterium"
+#> [52] "Arcticibacter"
+#> [53] "Asaccharospora"
+#> [54] "Asaia"
+#> [55] "Asinibacterium"
+#> [56] "Asteroleplasma"
+#> [57] "Asticcacaulis"
+#> [58] "Atopobium"
+#> [59] "Aureimonas"
+#> [60] "Azospira"
+#> [61] "Bacillus"
+#> [62] "Bacteriovorax"
+#> [63] "Bacteroides"
+#> [64] "Barnesiella"
+#> [65] "Bdellovibrio"
+#> [66] "Belnapia"
+#> [67] "Bergeyella"
+#> [68] "Bifidobacterium"
+#> [69] "Bilophila"
+#> [70] "Blastomonas"
+#> [71] "Blautia"
+#> [72] "Bordetella"
+#> [73] "Bosea"
+#> [74] "Brachybacterium"
+#> [75] "Bradyrhizobium"
+#> [76] "Brevibacterium"
+#> [77] "Brevundimonas"
+#> [78] "Brucella"
+#> [79] "Bulleidia"
+#> [80] "Burkholderia-Caballeronia-Paraburkholderia"
+#> [81] "Buttiauxella"
+#> [82] "Butyricicoccus"
+#> [83] "Butyricimonas"
+#> [84] "CAG-352"
+#> [85] "CAG-56"
+#> [86] "CAG-873"
+#> [87] "CHKCI001"
+#> [88] "CHKCI002"
+#> [89] "CL500-29 marine group"
+#> [90] "Caloribacterium"
+#> [91] "Campylobacter"
+#> [92] "Candidatus Arthromitus"
+#> [93] "Candidatus Metachlamydia"
+#> [94] "Candidatus Obscuribacter"
+#> [95] "Candidatus Phytoplasma"
+#> [96] "Candidatus Soleaferrea"
+#> [97] "Candidatus Stoquefichus"
+#> [98] "Capnocytophaga"
+#> [99] "Caproiciproducens"
+#> [100] "Cardiobacterium"
+#> [101] "Carnobacterium"
+#> [102] "Caryophanon"
+#> [103] "Castellaniella"
+#> [104] "Catabacter"
+#> [105] "Catenibacillus"
+#> [106] "Catenibacterium"
+#> [107] "Catenisphaera"
+#> [108] "Catonella"
+#> [109] "Caulobacter"
+#> [110] "Cellulomonas"
+#> [111] "Cellulosilyticum"
+#> [112] "Cellvibrio"
+#> [113] "Centipeda"
+#> [114] "Cetobacterium"
+#> [115] "Christensenella"
+#> [116] "Christensenellaceae R-7 group"
+#> [117] "Chryseobacterium"
+#> [118] "Chryseomicrobium"
+#> [119] "Chungangia"
+#> [120] "Citrobacter"
+#> [121] "Clavibacter"
+#> [122] "Cloacibacillus"
+#> [123] "Cloacibacterium"
+#> [124] "Clostridioides"
+#> [125] "Clostridium sensu stricto 1"
+#> [126] "Clostridium sensu stricto 12"
+#> [127] "Clostridium sensu stricto 13"
+#> [128] "Clostridium sensu stricto 15"
+#> [129] "Clostridium sensu stricto 18"
+#> [130] "Clostridium sensu stricto 2"
+#> [131] "Clostridium sensu stricto 3"
+#> [132] "Clostridium sensu stricto 4"
+#> [133] "Clostridium sensu stricto 6"
+#> [134] "Colidextribacter"
+#> [135] "Collinsella"
+#> [136] "Comamonas"
+#> [137] "Conexibacter"
+#> [138] "Conservatibacter"
+#> [139] "Coprobacillus"
+#> [140] "Coprobacter"
+#> [141] "Coprococcus"
+#> [142] "Coriobacteriaceae UCG-002"
+#> [143] "Corynebacterium"
+#> [144] "Cosenzaea"
+#> [145] "Criibacterium"
+#> [146] "Cryptobacterium"
+#> [147] "Curvibacter"
+#> [148] "Cutibacterium"
+#> [149] "Cytophaga"
+#> [150] "DNF00809"
+#> [151] "DSSD61"
+#> [152] "DTU089"
+#> [153] "Dechloromonas"
+#> [154] "Defluviicoccus"
+#> [155] "Defluviitaleaceae UCG-011"
+#> [156] "Delftia"
+#> [157] "Denitrobacterium"
+#> [158] "Dermabacter"
+#> [159] "Desemzia"
+#> [160] "Desulfovibrio"
+#> [161] "Devosia"
+#> [162] "Dialister"
+#> [163] "Diaphorobacter"
+#> [164] "Dickeya"
+#> [165] "Dielma"
+#> [166] "Dietzia"
+#> [167] "Dinghuibacter"
+#> [168] "Diplosphaera"
+#> [169] "Dolosigranulum"
+#> [170] "Dorea"
+#> [171] "Duganella"
+#> [172] "Dysgonomonas"
+#> [173] "Edaphobaculum"
+#> [174] "Eggerthella"
+#> [175] "Eikenella"
+#> [176] "Eisenbergiella"
+#> [177] "Empedobacter"
+#> [178] "Endobacter"
+#> [179] "Enhydrobacter"
+#> [180] "Enterobacter"
+#> [181] "Enterococcus"
+#> [182] "Enterorhabdus"
+#> [183] "Enteroscipio"
+#> [184] "Epulopiscium"
+#> [185] "Erwinia"
+#> [186] "Erysipelatoclostridium"
+#> [187] "Erysipelotrichaceae UCG-003"
+#> [188] "Erysipelotrichaceae UCG-006"
+#> [189] "Escherichia/Shigella"
+#> [190] "Eubacterium"
+#> [191] "Exiguobacterium"
+#> [192] "Extensimonas"
+#> [193] "F0058"
+#> [194] "F0332"
+#> [195] "FD2005"
+#> [196] "Facklamia"
+#> [197] "Faecalibacterium"
+#> [198] "Faecalicoccus"
+#> [199] "Faecalitalea"
+#> [200] "Falsochrobactrum"
+#> [201] "Family XIII AD3011 group"
+#> [202] "Family XIII UCG-001"
+#> [203] "Fictibacillus"
+#> [204] "Flaviflexus"
+#> [205] "Flavihumibacter"
+#> [206] "Flavobacterium"
+#> [207] "Flavonifractor"
+#> [208] "Floricoccus"
+#> [209] "Fluviicola"
+#> [210] "Fournierella"
+#> [211] "Fretibacterium"
+#> [212] "Frisingicoccus"
+#> [213] "Fructobacillus"
+#> [214] "Fusicatenibacter"
+#> [215] "Fusobacterium"
+#> [216] "GCA-900066575"
+#> [217] "GCA-900066755"
+#> [218] "Galbibacter"
+#> [219] "Garciella"
+#> [220] "Gemella"
+#> [221] "Gemmata"
+#> [222] "Geobacillus"
+#> [223] "Gluconobacter"
+#> [224] "Glutamicibacter"
+#> [225] "Gordonia"
+#> [226] "Gordonibacter"
+#> [227] "Granulicatella"
+#> [228] "Gulbenkiania"
+#> [229] "Haemophilus"
+#> [230] "Hafnia-Obesumbacterium"
+#> [231] "Halomonas"
+#> [232] "Haoranjiania"
+#> [233] "Harryflintia"
+#> [234] "Helicobacter"
+#> [235] "Hephaestia"
+#> [236] "Herbaspirillum"
+#> [237] "Herbinix"
+#> [238] "Holdemanella"
+#> [239] "Holdemania"
+#> [240] "Howardella"
+#> [241] "Hungatella"
+#> [242] "Hydrocarboniphaga"
+#> [243] "Hydrogenophilus"
+#> [244] "Hymenobacter"
+#> [245] "Iamia"
+#> [246] "Ignavigranum"
+#> [247] "Incertae Sedis [EUPATH_0009256_Bacteria_Firmicutes_Clostridia_Lachnospirales_Lachnospiraceae_Incertae_Sedis]"
+#> [248] "Incertae Sedis [EUPATH_0009256_Bacteria_Firmicutes_Clostridia_Oscillospirales_Ruminococcaceae_Incertae_Sedis]"
+#> [249] "Incertae Sedis [EUPATH_0009256_Bacteria_Proteobacteria_Gammaproteobacteria_Enterobacterales_Erwiniaceae_Incertae_Sedis]"
+#> [250] "Incertae Sedis [EUPATH_0009256_Bacteria_Proteobacteria_Gammaproteobacteria_Enterobacterales_Morganellaceae_Incertae_Sedis]"
+#> [251] "Intestinibacter"
+#> [252] "Intestinimonas"
+#> [253] "Janthinobacterium"
+#> [254] "Jeotgalicoccus"
+#> [255] "Johnsonella"
+#> [256] "Kingella"
+#> [257] "Klebsiella"
+#> [258] "Knoellia"
+#> [259] "Kocuria"
+#> [260] "Kosakonia"
+#> [261] "Lachnoanaerobaculum"
+#> [262] "Lachnobacterium"
+#> [263] "Lachnoclostridium"
+#> [264] "Lachnospira"
+#> [265] "Lachnospiraceae AC2044 group"
+#> [266] "Lachnospiraceae FCS020 group"
+#> [267] "Lachnospiraceae FE2018 group"
+#> [268] "Lachnospiraceae NC2004 group"
+#> [269] "Lachnospiraceae ND3007 group"
+#> [270] "Lachnospiraceae NK4A136 group"
+#> [271] "Lachnospiraceae UCG-001"
+#> [272] "Lachnospiraceae UCG-002"
+#> [273] "Lachnospiraceae UCG-003"
+#> [274] "Lachnospiraceae UCG-004"
+#> [275] "Lachnospiraceae UCG-008"
+#> [276] "Lachnospiraceae UCG-009"
+#> [277] "Lachnospiraceae UCG-010"
+#> [278] "Lachnospiraceae XPB1014 group"
+#> [279] "Lachnotalea"
+#> [280] "Lactobacillus"
+#> [281] "Lactococcus"
+#> [282] "Lactonifactor"
+#> [283] "Lautropia"
+#> [284] "Lawsonella"
+#> [285] "Legionella"
+#> [286] "Leptotrichia"
+#> [287] "Leuconostoc"
+#> [288] "Libanicoccus"
+#> [289] "Luteimonas"
+#> [290] "Luteolibacter"
+#> [291] "Macellibacteroides"
+#> [292] "Macrococcus"
+#> [293] "Mailhella"
+#> [294] "Mannheimia"
+#> [295] "Marinilactibacillus"
+#> [296] "Marmoricola"
+#> [297] "Martelella"
+#> [298] "Marvinbryantia"
+#> [299] "Massilia"
+#> [300] "Megamonas"
+#> [301] "Megasphaera"
+#> [302] "Merdibacter"
+#> [303] "Mesorhizobium"
+#> [304] "Methanobrevibacter"
+#> [305] "Methylibium"
+#> [306] "Methylobacillus"
+#> [307] "Methylobacterium-Methylorubrum"
+#> [308] "Methylorosula"
+#> [309] "Methylotenera"
+#> [310] "Micrococcus"
+#> [311] "Mitsuokella"
+#> [312] "Mobiluncus"
+#> [313] "Mogibacterium"
+#> [314] "Moheibacter"
+#> [315] "Mongoliitalea"
+#> [316] "Monoglobus"
+#> [317] "Moraxella"
+#> [318] "Morganella"
+#> [319] "Moryella"
+#> [320] "Mucilaginibacter"
+#> [321] "Muribaculum"
+#> [322] "Murimonas"
+#> [323] "Mycobacterium"
+#> [324] "Mycoplasma"
+#> [325] "Myxococcus"
+#> [326] "NK4A214 group"
+#> [327] "Nakamurella"
+#> [328] "Nannocystis"
+#> [329] "Necropsobacter"
+#> [330] "Negativibacillus"
+#> [331] "Negativicoccus"
+#> [332] "Neisseria"
+#> [333] "Neochlamydia"
+#> [334] "Neomegalonema"
+#> [335] "Neorhizobium"
+#> [336] "Neoscardovia"
+#> [337] "Nesterenkonia"
+#> [338] "Nocardioides"
+#> [339] "Nocardiopsis"
+#> [340] "Novosphingobium"
+#> [341] "Oceanivirga"
+#> [342] "Oceanobacillus"
+#> [343] "Ochrobactrum"
+#> [344] "Odoribacter"
+#> [345] "Olsenella"
+#> [346] "Oribacterium"
+#> [347] "Oscillibacter"
+#> [348] "Oscillospira"
+#> [349] "Ottowia"
+#> [350] "Oxalobacter"
+#> [351] "Oxobacter"
+#> [352] "P3OB-42"
+#> [353] "Paenibacillus"
+#> [354] "Paeniclostridium"
+#> [355] "Paenisporosarcina"
+#> [356] "Paludicola"
+#> [357] "Papillibacter"
+#> [358] "Parabacteroides"
+#> [359] "Paraclostridium"
+#> [360] "Paracoccus"
+#> [361] "Paramesorhizobium"
+#> [362] "Paraprevotella"
+#> [363] "Parapusillimonas"
+#> [364] "Parascardovia"
+#> [365] "Parasutterella"
+#> [366] "Parvibacter"
+#> [367] "Pasteurella"
+#> [368] "Paucibacter"
+#> [369] "Pediococcus"
+#> [370] "Pedobacter"
+#> [371] "Peptoclostridium"
+#> [372] "Peptococcus"
+#> [373] "Peptostreptococcus"
+#> [374] "Perlucidibaca"
+#> [375] "Phascolarctobacterium"
+#> [376] "Phaseolibacter"
+#> [377] "Phocea"
+#> [378] "Phoenicibacter"
+#> [379] "Phyllobacterium"
+#> [380] "Piscinibacter"
+#> [381] "Planifilum"
+#> [382] "Plesiomonas"
+#> [383] "Plot4-2H12"
+#> [384] "Pluralibacter"
+#> [385] "Polaromonas"
+#> [386] "Porphyromonas"
+#> [387] "Prevotella"
+#> [388] "Prevotellaceae NK3B31 group"
+#> [389] "Prevotellaceae UCG-001"
+#> [390] "Propionibacterium"
+#> [391] "Prosthecobacter"
+#> [392] "Proteus"
+#> [393] "Providencia"
+#> [394] "Pseudacidovorax"
+#> [395] "Pseudaminobacter"
+#> [396] "Pseudocitrobacter"
+#> [397] "Pseudoflavonifractor"
+#> [398] "Pseudoglutamicibacter"
+#> [399] "Pseudomonas"
+#> [400] "Pseudoramibacter"
+#> [401] "Pseudoxanthomonas"
+#> [402] "Psychrobacter"
+#> [403] "Pygmaiobacter"
+#> [404] "Pyramidobacter"
+#> [405] "Qipengyuania"
+#> [406] "Ralstonia"
+#> [407] "Raoultella"
+#> [408] "Raoultibacter"
+#> [409] "Reyranella"
+#> [410] "Rhizorhapis"
+#> [411] "Rhodanobacter"
+#> [412] "Rhodobacter"
+#> [413] "Rhodococcus"
+#> [414] "Rikenella"
+#> [415] "Rikenellaceae RC9 gut group"
+#> [416] "Rivicola"
+#> [417] "Robinsoniella"
+#> [418] "Rodentibacter"
+#> [419] "Romboutsia"
+#> [420] "Roseburia"
+#> [421] "Roseisolibacter"
+#> [422] "Rothia"
+#> [423] "Rubellimicrobium"
+#> [424] "Ruminococcus"
+#> [425] "Rummeliibacillus"
+#> [426] "S5-A14a"
+#> [427] "SH-PL14"
+#> [428] "Saccharothrix"
+#> [429] "Salinimicrobium"
+#> [430] "Salinisphaera"
+#> [431] "Salipaludibacillus"
+#> [432] "Salmonella"
+#> [433] "Sanguibacteroides"
+#> [434] "Sarcina"
+#> [435] "Scardovia"
+#> [436] "Sedimentibacter"
+#> [437] "Segetibacter"
+#> [438] "Selenomonas"
+#> [439] "Sellimonas"
+#> [440] "Senegalimassilia"
+#> [441] "Serratia"
+#> [442] "Shimwellia"
+#> [443] "Shuttleworthia"
+#> [444] "Slackia"
+#> [445] "Sneathia"
+#> [446] "Solibacillus"
+#> [447] "Solobacterium"
+#> [448] "Sphingoaurantiacus"
+#> [449] "Sphingobacterium"
+#> [450] "Sphingobium"
+#> [451] "Sphingomonas"
+#> [452] "Sphingopyxis"
+#> [453] "Sporolactobacillus"
+#> [454] "Staphylococcus"
+#> [455] "Stenotrophomonas"
+#> [456] "Stomatobaculum"
+#> [457] "Streptobacillus"
+#> [458] "Streptococcus"
+#> [459] "Subdoligranulum"
+#> [460] "Succinatimonas"
+#> [461] "Succiniclasticum"
+#> [462] "Succinivibrio"
+#> [463] "Sulfurospirillum"
+#> [464] "Sutterella"
+#> [465] "Synergistes"
+#> [466] "TM7x"
+#> [467] "Tannerella"
+#> [468] "Tatumella"
+#> [469] "Tepidimonas"
+#> [470] "Tepidiphilus"
+#> [471] "Terrisporobacter"
+#> [472] "Tetragenococcus"
+#> [473] "Thermus"
+#> [474] "Timonella"
+#> [475] "Tolumonas"
+#> [476] "Trabulsiella"
+#> [477] "Tropheryma"
+#> [478] "Trueperella"
+#> [479] "Turicibacter"
+#> [480] "Tuzzerella"
+#> [481] "Tyzzerella"
+#> [482] "UBA1819"
+#> [483] "UC5-1-2E3"
+#> [484] "UCG-002"
+#> [485] "UCG-003"
+#> [486] "UCG-004"
+#> [487] "UCG-005"
+#> [488] "UCG-007"
+#> [489] "UCG-008"
+#> [490] "UCG-009"
+#> [491] "Ureibacillus"
+#> [492] "Varibaculum"
+#> [493] "Variovorax"
+#> [494] "Veillonella"
+#> [495] "Verticiella"
+#> [496] "Victivallis"
+#> [497] "Vulcaniibacterium"
+#> [498] "Weissella"
+#> [499] "Xanthomonas"
+#> [500] "Yersinia"
+#> [501] "Yokenella"
+#> [502] "Zoogloea"
+#> [503] "[Bacteroides] pectinophilus group"
+#> [504] "[Clostridium] innocuum group"
+#> [505] "[Eubacterium] brachy group"
+#> [506] "[Eubacterium] eligens group"
+#> [507] "[Eubacterium] fissicatena group"
+#> [508] "[Eubacterium] hallii group"
+#> [509] "[Eubacterium] nodatum group"
+#> [510] "[Eubacterium] oxidoreducens group"
+#> [511] "[Eubacterium] ruminantium group"
+#> [512] "[Eubacterium] siraeum group"
+#> [513] "[Eubacterium] ventriosum group"
+#> [514] "[Eubacterium] xylanophilum group"
+#> [515] "[Ruminococcus] gauvreauii group"
+#> [516] "[Ruminococcus] gnavus group"
+#> [517] "[Ruminococcus] torques group"
+#> [518] "unclassified 0319-6G20"
+#> [519] "unclassified 67-14"
+#> [520] "unclassified A0839"
+#> [521] "unclassified Acetobacteraceae"
+#> [522] "unclassified Acidaminococcaceae"
+#> [523] "unclassified Actinobacteria"
+#> [524] "unclassified Actinomycetaceae"
+#> [525] "unclassified Aeromonadales"
+#> [526] "unclassified Anaerococcus"
+#> [527] "unclassified Anaerosalibacter"
+#> [528] "unclassified Anaerovoracaceae"
+#> [529] "unclassified Armatimonadales"
+#> [530] "unclassified Atopobiaceae"
+#> [531] "unclassified Bacillaceae"
+#> [532] "unclassified Bacillales"
+#> [533] "unclassified Bacilli"
+#> [534] "unclassified Bacteroidales"
+#> [535] "unclassified Bacteroidia"
+#> [536] "unclassified Barnesiellaceae"
+#> [537] "unclassified Bifidobacteriaceae"
+#> [538] "unclassified Burkholderiales"
+#> [539] "unclassified Butyricicoccaceae"
+#> [540] "unclassified Caloramatoraceae"
+#> [541] "unclassified Carnobacteriaceae"
+#> [542] "unclassified Caulobacteraceae"
+#> [543] "unclassified Chloroplast"
+#> [544] "unclassified Christensenellaceae"
+#> [545] "unclassified Chroococcidiopsaceae"
+#> [546] "unclassified Clostridia UCG-014"
+#> [547] "unclassified Clostridia"
+#> [548] "unclassified Clostridia vadinBB60 group"
+#> [549] "unclassified Clostridiaceae"
+#> [550] "unclassified Clostridiales"
+#> [551] "unclassified Comamonadaceae"
+#> [552] "unclassified Coriobacteriales Incertae Sedis"
+#> [553] "unclassified Coriobacteriales"
+#> [554] "unclassified Corynebacteriaceae"
+#> [555] "unclassified Desulfovibrionaceae"
+#> [556] "unclassified Devosiaceae"
+#> [557] "unclassified Diplorickettsiaceae"
+#> [558] "unclassified Eggerthellaceae"
+#> [559] "unclassified Enterobacterales"
+#> [560] "unclassified Enterobacteriaceae"
+#> [561] "unclassified Enterococcaceae"
+#> [562] "unclassified Erwiniaceae"
+#> [563] "unclassified Erysipelatoclostridiaceae"
+#> [564] "unclassified Erysipelotrichaceae"
+#> [565] "unclassified Erysipelotrichales"
+#> [566] "unclassified Ethanoligenenaceae"
+#> [567] "unclassified Eubacteriaceae"
+#> [568] "unclassified Ezakiella"
+#> [569] "unclassified Fastidiosipila"
+#> [570] "unclassified Fenollaria"
+#> [571] "unclassified Fimbriimonadaceae"
+#> [572] "unclassified Finegoldia"
+#> [573] "unclassified Firmicutes"
+#> [574] "unclassified Flavobacteriaceae"
+#> [575] "unclassified Flavobacteriales"
+#> [576] "unclassified Fusobacteriaceae"
+#> [577] "unclassified Gaiellales"
+#> [578] "unclassified Gallicola"
+#> [579] "unclassified Gammaproteobacteria"
+#> [580] "unclassified Gastranaerophilales"
+#> [581] "unclassified Gemmataceae"
+#> [582] "unclassified Hungateiclostridiaceae"
+#> [583] "unclassified Hydrogenoanaerobacterium"
+#> [584] "unclassified Izemoplasmatales"
+#> [585] "unclassified JI49D030"
+#> [586] "unclassified KD3-93"
+#> [587] "unclassified Kapabacteriales"
+#> [588] "unclassified Lachnospiraceae"
+#> [589] "unclassified Lachnospirales"
+#> [590] "unclassified Lactobacillales"
+#> [591] "unclassified Leuconostocaceae"
+#> [592] "unclassified Lineage IV"
+#> [593] "unclassified MAT-CR-H4-C10"
+#> [594] "unclassified Methylococcaceae"
+#> [595] "unclassified Micavibrionales"
+#> [596] "unclassified Microbacteriaceae"
+#> [597] "unclassified Micrococcaceae"
+#> [598] "unclassified Micrococcales"
+#> [599] "unclassified Mitochondria"
+#> [600] "unclassified Moraxellaceae"
+#> [601] "unclassified Murdochiella"
+#> [602] "unclassified Muribaculaceae"
+#> [603] "unclassified NS9 marine group"
+#> [604] "unclassified Neisseriaceae"
+#> [605] "unclassified OLB14"
+#> [606] "unclassified Opitutales"
+#> [607] "unclassified Oscillospiraceae"
+#> [608] "unclassified Oscillospirales"
+#> [609] "unclassified Oxalobacteraceae"
+#> [610] "unclassified P5D1-392"
+#> [611] "unclassified PLTA13"
+#> [612] "unclassified Paenibacillaceae"
+#> [613] "unclassified Paracaedibacteraceae"
+#> [614] "unclassified Parachlamydiaceae"
+#> [615] "unclassified Parvimonas"
+#> [616] "unclassified Pasteurellaceae"
+#> [617] "unclassified Peptococcaceae"
+#> [618] "unclassified Peptoniphilus"
+#> [619] "unclassified Peptostreptococcaceae"
+#> [620] "unclassified Peptostreptococcales-Tissierellales"
+#> [621] "unclassified Planctomycetales"
+#> [622] "unclassified Planococcaceae"
+#> [623] "unclassified Prevotellaceae"
+#> [624] "unclassified Promicromonosporaceae"
+#> [625] "unclassified Propionibacteriaceae"
+#> [626] "unclassified Proteobacteria"
+#> [627] "unclassified Pseudomonadaceae"
+#> [628] "unclassified Puniceicoccaceae"
+#> [629] "unclassified RF39"
+#> [630] "unclassified Rhizobiaceae"
+#> [631] "unclassified Rhizobiales Incertae Sedis"
+#> [632] "unclassified Rhizobiales"
+#> [633] "unclassified Rhodobacteraceae"
+#> [634] "unclassified Rhodocyclaceae"
+#> [635] "unclassified Rhodospirillales"
+#> [636] "unclassified Rickettsiales"
+#> [637] "unclassified Rikenellaceae"
+#> [638] "unclassified Ruminiclostridium"
+#> [639] "unclassified Ruminococcaceae"
+#> [640] "unclassified ST-12K33"
+#> [641] "unclassified Saccharimonadales"
+#> [642] "unclassified Sandaracinaceae"
+#> [643] "unclassified Selenomonadaceae"
+#> [644] "unclassified Simkaniaceae"
+#> [645] "unclassified Solimonadaceae"
+#> [646] "unclassified Sphingobacteriales"
+#> [647] "unclassified Sphingomonadaceae"
+#> [648] "unclassified Staphylococcaceae"
+#> [649] "unclassified Streptococcaceae"
+#> [650] "unclassified Succinivibrionaceae"
+#> [651] "unclassified Sutterellaceae"
+#> [652] "unclassified TRA3-20"
+#> [653] "unclassified Tannerellaceae"
+#> [654] "unclassified Tepidimicrobium"
+#> [655] "unclassified UCG-010"
+#> [656] "unclassified UCG-011"
+#> [657] "unclassified Veillonellaceae"
+#> [658] "unclassified Veillonellales-Selenomonadales"
+#> [659] "unclassified Vermiphilaceae"
+#> [660] "unclassified Verrucomicrobiales"
+#> [661] "unclassified Verrucomicrobiota"
+#> [662] "unclassified Victivallaceae"
+#> [663] "unclassified W5053"
+#> [664] "unclassified WPS-2"
+#> [665] "unclassified Weeksellaceae"
+#> [666] "unclassified Xanthobacteraceae"
+#> [667] "unclassified Yersiniaceae"
+#> [668] "unclassified [Clostridium] methylpentosum group"
+#> [669] "unclassified [Eubacterium] coprostanoligenes group"
+#> [670] "unclassified vadinBE97"
+getMetadataVariableNames(microbiomeData::DiabImmune)
+#> [1] "Participant_Id"
+#> [2] "Participant_repeated_measure_Id"
+#> [3] "age_1st_animal_milk_or_solids_given_days"
+#> [4] "age_1st_given_apple_months"
+#> [5] "age_1st_given_banana_months"
+#> [6] "age_1st_given_barley_months"
+#> [7] "age_1st_given_beef_months"
+#> [8] "age_1st_given_berries_months"
+#> [9] "age_1st_given_cabbs_months"
+#> [10] "age_1st_given_carrot_months"
+#> [11] "age_1st_given_corn_months"
+#> [12] "age_1st_given_cowsmilk_months"
+#> [13] "age_1st_given_egg_months"
+#> [14] "age_1st_given_fish_months"
+#> [15] "age_1st_given_milk_products_months"
+#> [16] "age_1st_given_oat_months"
+#> [17] "age_1st_given_pear_months"
+#> [18] "age_1st_given_peas_months"
+#> [19] "age_1st_given_plum_months"
+#> [20] "age_1st_given_pork_months"
+#> [21] "age_1st_given_potato_months"
+#> [22] "age_1st_given_poultry_months"
+#> [23] "age_1st_given_rice_months"
+#> [24] "age_1st_given_rye_months"
+#> [25] "age_1st_given_sweet_potato_months"
+#> [26] "age_1st_given_tomato_months"
+#> [27] "age_1st_given_wheat_months"
+#> [28] "age_at_anthropometry_days"
+#> [29] "age_at_two_autoantibodies_positive_days"
+#> [30] "age_at_type_1_diabetes_diagnosis_days"
+#> [31] "antibiotics_before_delivery_by_maternal_report"
+#> [32] "bmi_minus_for_minus_age_z_minus_score"
+#> [33] "breastfed_duration_days"
+#> [34] "country"
+#> [35] "delivery_mode"
+#> [36] "diet_in_first_three_days"
+#> [37] "exclusive_breastfed_duration_days"
+#> [38] "gestational_diabetes_by_maternal_report"
+#> [39] "glutamic_acid_decarboxylase_autoantibodies"
+#> [40] "hla_risk_by_hla_haplotyping"
+#> [41] "height_minus_for_minus_age_z_minus_score"
+#> [42] "insulin_autoantibodies"
+#> [43] "insulinoma_minus_associated_protein_2_autoantibodies"
+#> [44] "islet_cell_autoantibodies"
+#> [45] "linear_growth_during_1st_year_cm"
+#> [46] "maternal_age_at_birth_months"
+#> [47] "mean_linear_growth_during_1st_3_years"
+#> [48] "mean_weight_gain_during_1st_3_years"
+#> [49] "sex"
+#> [50] "study_group"
+#> [51] "type_1_diabetes_diagnosed"
+#> [52] "urban_or_rural_site"
+#> [53] "weight_gain_during_1st_year_kg"
+#> [54] "weight_minus_for_minus_age_z_minus_score"
+#> [55] "zinc_transporter_8_autoantibodies"
+#> [56] "age_months"
+#> [57] "Sample_Id"
+#> [58] "habitat"
+#> [59] "host_body_habitat"
+#> [60] "host_body_product"
+#> [61] "host_body_site"
+#> [62] "sample_type"
+variablesDT <- getVariables(
+ microbiomeData::DiabImmune,
+ list("metadata" = c("age_months", "sex"),
+ "16S (V4) Genus" = "Bacteroides",
+ "WGS Metagenome enzyme pathway abundance data" = "ANAGLYCOLYSIS-PWY: glycolysis III (from glucose)"
+ )
+)
+#>
+#> 2024-04-24 16:51:15.706984 Removed 300 records with no data.
+
+