diff --git a/NAMESPACE b/NAMESPACE index afcdffc..e8a3045 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -25,6 +25,7 @@ export(PlotUcellCorrelation) export(PredictCellTypeProbability) export(PredictTcellActivation) export(PredictTcellActivationUsingCustomModel) +export(RegisterGeneSet) export(RunCellTypist) export(RunScGate) export(RunScGateForModels) diff --git a/R/Phenotyping.R b/R/Phenotyping.R index c83a298..82e1639 100644 --- a/R/Phenotyping.R +++ b/R/Phenotyping.R @@ -318,7 +318,13 @@ PlotMarkerSet <- function(seuratObj, reductions, title, features) { pkg.env$GENE_SETS <- list() -.RegisterGeneSet <- function(name, genes) { +#' @title RegisterGeneSet +#' +#' @description Registers a named gene set in the package gene-set registry. +#' @param name The name of the gene set +#' @param genes A character vector of gene names +#' @export +RegisterGeneSet <- function(name, genes) { if (name %in% names(pkg.env$GENE_SETS)) { stop(paste0('Name has already been registered: ', name)) } @@ -341,109 +347,111 @@ GetGeneSet <- function(name) { } ### Begin Phenotyping Gene Sets -.RegisterGeneSet('TandNK_Activation.1', c('CCL4L1','MIR155HG','RGCC','NFKBIA','IFNG','NR4A3','TNFSF14','CCL3')) +RegisterGeneSet('TandNK_Activation.1', c('CCL4L1','MIR155HG','RGCC','NFKBIA','IFNG','NR4A3','TNFSF14','CCL3')) -.RegisterGeneSet('TandNK_Activation.Core', c('CCL4L1','LOC100430627', 'IFNG','NR4A3','TNFSF14','CCL3', 'LOC100423131')) +RegisterGeneSet('TandNK_Activation.Core', c('CCL4L1','LOC100430627', 'IFNG','NR4A3','TNFSF14','CCL3', 'LOC100423131')) -.RegisterGeneSet('TandNK_Activation.2', c('TNFRSF14', 'CCL3', 'CCL4L1', 'NFKBID','IFNG', 'TNF')) +RegisterGeneSet('TandNK_Activation.2', c('TNFRSF14', 'CCL3', 'CCL4L1', 'NFKBID','IFNG', 'TNF')) -.RegisterGeneSet('TandNK_Activation.3', c('CD82', 'IRF8', 'TNFRSF9', 'PIGT', 'IRF4', 'XCL1', 'IL2RA', 'CCL3')) +RegisterGeneSet('TandNK_Activation.3', c('CD82', 'IRF8', 'TNFRSF9', 'PIGT', 'IRF4', 'XCL1', 'IL2RA', 'CCL3')) # This is based on T-cell analysis from lung T/NK cells. This my not be precisely Memory/Naive. -.RegisterGeneSet('MemoryAndNaive', c('SELL', 'IL7R', 'LTB', 'SPOCK2', 'COTL1', 'JUNB', 'GPR183', 'CCR7', 'FUOM', 'CD7', 'PECAM1')) +RegisterGeneSet('MemoryAndNaive', c('SELL', 'IL7R', 'LTB', 'SPOCK2', 'COTL1', 'JUNB', 'GPR183', 'CCR7', 'FUOM', 'CD7', 'PECAM1')) -.RegisterGeneSet('Cytotoxicity.1', c('PRF1', 'GNLY', 'NKG7', 'GZMA', 'GZMB', 'GZMH', 'GZMK', 'GZMM')) -.RegisterGeneSet('Cytotoxicity.2', c('PRF1', 'GNLY', 'GZMB', 'CTSW')) -.RegisterGeneSet('Cytotoxicity.3', c('PRF1', 'GNLY', 'GZMA', 'GZMB', 'GZMH', 'GZMK', 'GZMM', 'CTSW')) +RegisterGeneSet('Cytotoxicity.1', c('PRF1', 'GNLY', 'NKG7', 'GZMA', 'GZMB', 'GZMH', 'GZMK', 'GZMM')) +RegisterGeneSet('Cytotoxicity.2', c('PRF1', 'GNLY', 'GZMB', 'CTSW')) +RegisterGeneSet('Cytotoxicity.3', c('PRF1', 'GNLY', 'GZMA', 'GZMB', 'GZMH', 'GZMK', 'GZMM', 'CTSW')) -.RegisterGeneSet('Cytotoxicity.GzmABH', c('GZMA','GZMB','GZMH')) -.RegisterGeneSet('Cytotoxicity.GzmKM', c('GZMK','GZMM')) -.RegisterGeneSet('Metallothionein', c('MT1A', 'MT1E', 'MT1M', 'MT1X', 'MT2A', 'MT1JP')) -.RegisterGeneSet('Metallothionein.Core', c('MT1E', 'MT1M', 'MT1X', 'MT2A')) -.RegisterGeneSet('IEGs', c('FOS', 'JUN', 'ZFP36')) -.RegisterGeneSet('TCellMemoryS100', c('S100A4', 'S100A6','S100A10','S100A11')) +RegisterGeneSet('Cytotoxicity.GzmABH', c('GZMA','GZMB','GZMH')) +RegisterGeneSet('Cytotoxicity.GzmKM', c('GZMK','GZMM')) +RegisterGeneSet('Metallothionein', c('MT1A', 'MT1E', 'MT1M', 'MT1X', 'MT2A', 'MT1JP')) +RegisterGeneSet('Metallothionein.Core', c('MT1E', 'MT1M', 'MT1X', 'MT2A')) +RegisterGeneSet('IEGs', c('FOS', 'JUN', 'ZFP36')) +RegisterGeneSet('TCellMemoryS100', c('S100A4', 'S100A6','S100A10','S100A11')) -.RegisterGeneSet('EffectorT', c('CCL4L1','CCL5','CCR7-','CD7-','FUOM-','GNLY','GZMB','GZMH','HOPX','LTB-','NKG7','PECAM1-','PRF1','RGS9','S100A4','SELL-','SPOCK2-','JUNB-')) +RegisterGeneSet('EffectorT', c('CCL4L1','CCL5','CCR7-','CD7-','FUOM-','GNLY','GZMB','GZMH','HOPX','LTB-','NKG7','PECAM1-','PRF1','RGS9','S100A4','SELL-','SPOCK2-','JUNB-')) -.RegisterGeneSet('CentralMemT', c('CCR7', 'CLDND1', 'GPR183')) +RegisterGeneSet('CentralMemT', c('CCR7', 'CLDND1', 'GPR183')) # Note: 'CD7', 'CCR7' excluded since they are in Tcm as well -.RegisterGeneSet('NaiveT', c('CTSH', 'CA6', 'GSTT1', 'LEF1','RGS10', 'TMIGD2')) +RegisterGeneSet('NaiveT', c('CTSH', 'CA6', 'GSTT1', 'LEF1','RGS10', 'TMIGD2')) -.RegisterGeneSet('CD8Memory', c('CD8A', 'CST7', 'CTSW', 'GNLY', 'GZMK')) +RegisterGeneSet('CD8Memory', c('CD8A', 'CST7', 'CTSW', 'GNLY', 'GZMK')) -.RegisterGeneSet('InterferonAndCytokines', c('IFNA1', 'IFNA2', 'IFNB1', 'IL6', 'IFNG', 'TNF', 'CCL3', 'CCL3L1', 'CCL4', 'CCL4L1')) +RegisterGeneSet('InterferonAndCytokines', c('IFNA1', 'IFNA2', 'IFNB1', 'IL6', 'IFNG', 'TNF', 'CCL3', 'CCL3L1', 'CCL4', 'CCL4L1')) -.RegisterGeneSet('Interleukins', c('IL1', 'IL2', 'IL3', 'IL4', 'IL5', 'IL6', 'IL7', 'CXCL8', 'IL9', 'IL10', 'IL11', 'IL13', 'TXLNA', 'IL15', 'IL16', 'IL17A', 'IL17B', 'IL18', 'IL19', 'IL20', 'IL21', 'IL22')) +RegisterGeneSet('Interleukins', c('IL1', 'IL2', 'IL3', 'IL4', 'IL5', 'IL6', 'IL7', 'CXCL8', 'IL9', 'IL10', 'IL11', 'IL13', 'TXLNA', 'IL15', 'IL16', 'IL17A', 'IL17B', 'IL18', 'IL19', 'IL20', 'IL21', 'IL22')) -.RegisterGeneSet('InterleukinReceptors', c('IL1R1','IL1R2','IL2RA','IL2RB','IL2RG','IL3RA','IL4R','IL5RA','IL6R','IL7R','IL10RA','IL12RB1','IL12RB2','IL13RA2','IL15RA','IL17RA','IL17RB','IL17RC','IL17RD','IL17RE','IL20RA','IL20RB','IL21R','IL22RA2','IL27RA','IL31RA')) +RegisterGeneSet('InterleukinReceptors', c('IL1R1','IL1R2','IL2RA','IL2RB','IL2RG','IL3RA','IL4R','IL5RA','IL6R','IL7R','IL10RA','IL12RB1','IL12RB2','IL13RA2','IL15RA','IL17RA','IL17RB','IL17RC','IL17RD','IL17RE','IL20RA','IL20RB','IL21R','IL22RA2','IL27RA','IL31RA')) # https://www.frontiersin.org/journals/genetics/articles/10.3389/fgene.2024.1389630/full # TNFRSF6 = Fas -.RegisterGeneSet('Apoptosis', c('FASLG', 'FAS', 'BCL2', 'IRF9', 'JAK3', 'CASP3', 'CASP8', 'BAX', 'TNFRSF1A', 'TP53', 'CYCS', 'PARP1')) +RegisterGeneSet('Apoptosis', c('FASLG', 'FAS', 'BCL2', 'IRF9', 'JAK3', 'CASP3', 'CASP8', 'BAX', 'TNFRSF1A', 'TP53', 'CYCS', 'PARP1')) -.RegisterGeneSet('EffectorCytokines', c('IFNG', 'TNF', 'IL17A', 'IL2', 'CSF1', 'CSF2', 'CCL3', 'CCL3L1', 'CCL4', 'CCL4L1')) -.RegisterGeneSet('ExhaustionOrInhibitory', c('PDCD1', 'TIGIT', 'HAVCR2', 'LAG3', 'CTLA4', 'VTCN1', 'CD244', 'KLRG1', 'TNFRSF14', 'BTLA', 'CD160')) +RegisterGeneSet('EffectorCytokines', c('IFNG', 'TNF', 'IL17A', 'IL2', 'CSF1', 'CSF2', 'CCL3', 'CCL3L1', 'CCL4', 'CCL4L1')) +RegisterGeneSet('ExhaustionOrInhibitory', c('PDCD1', 'TIGIT', 'HAVCR2', 'LAG3', 'CTLA4', 'VTCN1', 'CD244', 'KLRG1', 'TNFRSF14', 'BTLA', 'CD160')) -.RegisterGeneSet('Myelocytes', c("OLFM4", "LTF", "CAMP", "LCN2")) -.RegisterGeneSet('Pro_Myelocytes', c("BPI", "MPO", "ELANE", "RTD1A", "RTD1B", "DEFA1B", "AZU1")) +RegisterGeneSet('Myelocytes', c("OLFM4", "LTF", "CAMP", "LCN2")) +RegisterGeneSet('Pro_Myelocytes', c("BPI", "MPO", "ELANE", "RTD1A", "RTD1B", "DEFA1B", "AZU1")) #These were found by literature investigation, and the MCMs were added via correlation with UNG - a necessary gene for somatic hypermutation. -.RegisterGeneSet('SomaticHypermutation', c("AICDA", "UNG", "MCM5", "MCM4", "MCM3", "MCM6", "MCM2")) +RegisterGeneSet('SomaticHypermutation', c("AICDA", "UNG", "MCM5", "MCM4", "MCM3", "MCM6", "MCM2")) #These BCell signatures were compiled by Greg for use in RIRA (evidence is literature support & marker-uniqueness within RIRA) -.RegisterGeneSet("GerminalCenter", c("AICDA", "RGS13", "MEF2B", "ELL3", "FAS")) #CD40 omitted -.RegisterGeneSet("CD40_Pos_BCells", c("CD69", "AHNAK", "MAMU-DRA", "MS4A1", "CD1C")) #this is a weak signature, with some overlap between CD40- B cells. This should be supplemented with Memory vs Naive gene sets. -.RegisterGeneSet("CD40_Neg_BCells", c("ANHAK", "SOX5", "MAMU-DRA", "MS4A1", "CD1C")) #similarly, this signature has overlap with CD40+. -.RegisterGeneSet("Pre-BCells", c("STMN1", "VPREB1", "SOX4")) -.RegisterGeneSet("PlasmaCells", c("DERL3", "TNFRSF17", "JCHAIN", "FKBP11", "XBP1")) #I omitted IGHA1, since we should probably keep this gene set class agnostic. -.RegisterGeneSet("NaiveB", c("TCL1A", "FCER2", "CXCR4")) -.RegisterGeneSet("MemoryB", c("CR2", "PLAC8", "LY86", "CD44")) -.RegisterGeneSet("InnateB", c("CD1C", "AHNAK", "SOX5")) +RegisterGeneSet("GerminalCenter", c("AICDA", "RGS13", "MEF2B", "ELL3", "FAS")) #CD40 omitted +RegisterGeneSet("CD40_Pos_BCells", c("CD69", "AHNAK", "MAMU-DRA", "MS4A1", "CD1C")) #this is a weak signature, with some overlap between CD40- B cells. This should be supplemented with Memory vs Naive gene sets. +RegisterGeneSet("CD40_Neg_BCells", c("ANHAK", "SOX5", "MAMU-DRA", "MS4A1", "CD1C")) #similarly, this signature has overlap with CD40+. +RegisterGeneSet("Pre-BCells", c("STMN1", "VPREB1", "SOX4")) +RegisterGeneSet("PlasmaCells", c("DERL3", "TNFRSF17", "JCHAIN", "FKBP11", "XBP1")) #I omitted IGHA1, since we should probably keep this gene set class agnostic. +RegisterGeneSet("NaiveB", c("TCL1A", "FCER2", "CXCR4")) +RegisterGeneSet("MemoryB", c("CR2", "PLAC8", "LY86", "CD44")) +RegisterGeneSet("InnateB", c("CD1C", "AHNAK", "SOX5")) +# Cell-cycle / proliferation +RegisterGeneSet('Proliferation', c('MKI67', 'TOP2A')) ### End Phenotyping Gene Sets # Sustaining CD4 survival? # TNFRSF4 = OX40 # TNFSF4 = OX40L -.RegisterGeneSet('MMul10TcrConstantRegion', c('LOC710951', 'LOC114677140', 'LOC711031', 'LOC720538', 'LOC705095')) +RegisterGeneSet('MMul10TcrConstantRegion', c('LOC710951', 'LOC114677140', 'LOC711031', 'LOC720538', 'LOC705095')) -.RegisterGeneSet('MAIT_Markers', c('KLRB1', 'CEPBD', 'NCR3', 'ZBTB16', 'RORC', 'SLC4A10', 'DPP4')) +RegisterGeneSet('MAIT_Markers', c('KLRB1', 'CEPBD', 'NCR3', 'ZBTB16', 'RORC', 'SLC4A10', 'DPP4')) # Dysfunction? # 'MT1A', 'MT2A', 'MT1M' -.RegisterGeneSet('MMul10TcrGenes', c('LOC703029','LOC696306','LOC106999340','LOC106996262','LOC106999345','LOC106997707','LOC106997706','LOC710149','LOC700771','LOC699427','LOC711871','LOC709081','LOC698785','LOC114677052','LOC114676933','LOC106999353','LOC106999351','LOC106999350','LOC106999349','LOC106999348','LOC106999347','LOC106999346','LOC106999343','LOC106999341','LOC106999339','LOC106999337','LOC106999336','LOC106999335','LOC106999312','LOC106997705','LOC106997704','LOC106997703','LOC106997702','LOC106997697','LOC106997453','LOC106997452','LOC106997451','LOC106995765','LOC106992460','LOC106992446','LOC106992434','LOC106992433','LOC720456','LOC716949','LOC716866','LOC711537','LOC711386','LOC711194','LOC711141','LOC711066','LOC710821','LOC710627','LOC710455','LOC710361','LOC710183','LOC710093','LOC709531','LOC708581','LOC708328','LOC704883','LOC703153','LOC702904','LOC702550','LOC702113','LOC701992','LOC701875','LOC701745','LOC701395','LOC701262','LOC701152','LOC700224','LOC700154','LOC700105','LOC699912','LOC699790','LOC699543','LOC699298','LOC699162','LOC698913','LOC698543','LOC698289','LOC698161','LOC697792','LOC697466','LOC697234','LOC697054','LOC696752','LOC696684','LOC696557','LOC696075','LOC695943','LOC114679533','LOC114679531','LOC114677139','LOC114677137','LOC114677136','LOC114677055','LOC114677054','LOC114677050','LOC114677049','LOC114677047','LOC114675766')) -.RegisterGeneSet("MMul10_MHC", c("MAMU-A", "MAMU-A3", "MAMU-AG", "LOC719250", "LOC100426197", "LOC714466", "LOC694372", "LOC114677644", "LOC114675360", "LOC106997902", "LOC698738", "LOC106996077", "LOC106992378", "LOC100424348", "LOC106995519", "LOC106992468", "LOC114676051", "LOC106996627", "LOC106997893", "LOC106997885", "LOC114675646", "LOC114669738", "LOC720132", "LOC719702", "LOC106996676", "LOC714964", "LOC114669810", "LOC114675357", "LOC100428435", "LOC100429195", "LOC699987", "LOC114677642", "LOC723473", "LOC106995461", "LOC106995452")) -.RegisterGeneSet("MMul10_KIR", c("KIR3DL0", "KIR3DL2", "KIR2DS4", "KIR2DL4", "KIR3DS05", "KIR3DL12", "KIR3DL1", "KIR3DH", "KIR3DH5", "KIR3DL21", "KIR3DL11", "MAMU-KIR", "LOC106994859", "LOC114669735", "LOC100424026", "LOC100125572")) +RegisterGeneSet('MMul10TcrGenes', c('LOC703029','LOC696306','LOC106999340','LOC106996262','LOC106999345','LOC106997707','LOC106997706','LOC710149','LOC700771','LOC699427','LOC711871','LOC709081','LOC698785','LOC114677052','LOC114676933','LOC106999353','LOC106999351','LOC106999350','LOC106999349','LOC106999348','LOC106999347','LOC106999346','LOC106999343','LOC106999341','LOC106999339','LOC106999337','LOC106999336','LOC106999335','LOC106999312','LOC106997705','LOC106997704','LOC106997703','LOC106997702','LOC106997697','LOC106997453','LOC106997452','LOC106997451','LOC106995765','LOC106992460','LOC106992446','LOC106992434','LOC106992433','LOC720456','LOC716949','LOC716866','LOC711537','LOC711386','LOC711194','LOC711141','LOC711066','LOC710821','LOC710627','LOC710455','LOC710361','LOC710183','LOC710093','LOC709531','LOC708581','LOC708328','LOC704883','LOC703153','LOC702904','LOC702550','LOC702113','LOC701992','LOC701875','LOC701745','LOC701395','LOC701262','LOC701152','LOC700224','LOC700154','LOC700105','LOC699912','LOC699790','LOC699543','LOC699298','LOC699162','LOC698913','LOC698543','LOC698289','LOC698161','LOC697792','LOC697466','LOC697234','LOC697054','LOC696752','LOC696684','LOC696557','LOC696075','LOC695943','LOC114679533','LOC114679531','LOC114677139','LOC114677137','LOC114677136','LOC114677055','LOC114677054','LOC114677050','LOC114677049','LOC114677047','LOC114675766')) +RegisterGeneSet("MMul10_MHC", c("MAMU-A", "MAMU-A3", "MAMU-AG", "LOC719250", "LOC100426197", "LOC714466", "LOC694372", "LOC114677644", "LOC114675360", "LOC106997902", "LOC698738", "LOC106996077", "LOC106992378", "LOC100424348", "LOC106995519", "LOC106992468", "LOC114676051", "LOC106996627", "LOC106997893", "LOC106997885", "LOC114675646", "LOC114669738", "LOC720132", "LOC719702", "LOC106996676", "LOC714964", "LOC114669810", "LOC114675357", "LOC100428435", "LOC100429195", "LOC699987", "LOC114677642", "LOC723473", "LOC106995461", "LOC106995452")) +RegisterGeneSet("MMul10_KIR", c("KIR3DL0", "KIR3DL2", "KIR2DS4", "KIR2DL4", "KIR3DS05", "KIR3DL12", "KIR3DL1", "KIR3DH", "KIR3DH5", "KIR3DL21", "KIR3DL11", "MAMU-KIR", "LOC106994859", "LOC114669735", "LOC100424026", "LOC100125572")) # Generated using: sort(rownames(seuratObj@assays$RNA)[grepl(rownames(seuratObj@assays$RNA), pattern = '^RP[SL]')]) ribosomalGenes <- c("RPL10", "RPL10A", "RPL10L", "RPL11", "RPL12", "RPL13", "RPL13A", "RPL14", "RPL15", "RPL17", "RPL18", "RPL18A", "RPL19", "RPL21", "RPL22", "RPL22L1", "RPL23", "RPL23A", "RPL24", "RPL26", "RPL26L1", "RPL27", "RPL27A", "RPL28", "RPL29", "RPL3", "RPL30", "RPL31", "RPL32", "RPL34", "RPL35", "RPL35A", "RPL36", "RPL36AL", "RPL37", "RPL37A", "RPL37A-1", "RPL38", "RPL39", "RPL39L", "RPL3L", "RPL4", "RPL41", "RPL5", "RPL6", "RPL7", "RPL7A", "RPL7L1", "RPL8", "RPL9", "RPLP0", "RPLP1", "RPLP2", "RPS10", "RPS11", "RPS12", "RPS13", "RPS14", "RPS15", "RPS15A", "RPS16", "RPS17", "RPS18", "RPS19", "RPS19BP1", "RPS2", "RPS20", "RPS21", "RPS23", "RPS24", "RPS25", "RPS26", "RPS27", "RPS27A", "RPS27A-1", "RPS27L", "RPS28", "RPS29", "RPS3", "RPS4X", "RPS4Y1", "RPS4Y2", "RPS5", "RPS6KA1", "RPS6KA2", "RPS6KA3", "RPS6KA4", "RPS6KA5", "RPS6KA6", "RPS6KB1", "RPS6KB2", "RPS6KC1", "RPS6KL1", "RPS7", "RPS8", "RPS9", "RPSA") # These were identified by grep on the descriptions of all LOC* genes for ribosomal ribosomalGenes <- c(ribosomalGenes, c("LOC717349", "LOC718596", "LOC705988", "LOC703571", "LOC100429589", "LOC114672439", "LOC711644", "LOC705840", "LOC114674534", "LOC697510", "LOC100426562", "LOC100430397", "LOC705494", "LOC718356", "LOC708673", "LOC708221", "LOC693728", "LOC701224", "LOC695949", "LOC100430766", "LOC708539", "LOC114670541", "LOC694687", "LOC696921", "LOC106999910", "LOC705621", "LOC706532", "LOC701369", "LOC106994001", "LOC114675582", "LOC706087", "LOC711318", "LOC695920", "LOC697723", "LOC700257", "LOC710331", "LOC700807", "LOC106992793", "LOC717846", "LOC694712", "LOC708815", "LOC702606", "LOC707204", "LOC106996615", "LOC711714", "LOC697734", "LOC100425632", "LOC709255", "LOC703037", "LOC710558", "LOC114670812", "LOC721996", "LOC716997", "LOC698732", "LOC702174", "LOC114679384", "LOC697431", "LOC704429", "LOC106992303", "LOC114676316", "LOC100430733", "LOC708154", "LOC114673092", "LOC697548", "LOC695895", "LOC708833", "LOC701909", "LOC715154", "LOC717289", "LOC106998255", "LOC701084", "LOC707369", "LOC697035", "LOC720167", "LOC700616", "LOC700401", "LOC106996191", "LOC106998695", "LOC707090", "LOC717450", "LOC693713", "LOC713382", "LOC716142", "LOC696119", "LOC714106", "LOC695421", "LOC709128", "LOC714782", "LOC693486", "LOC106992469", "LOC699246", "LOC708791", "LOC699630", "LOC697141", "LOC710726", "LOC107000432", "LOC100428100", "LOC718153", "LOC100427366", "LOC693343", "LOC114669718", "LOC713514", "LOC698010", "LOC715166", "LOC695327", "LOC702713", "LOC704640", "LOC114674200", "LOC700134", "LOC715041", "LOC722876", "LOC710644", "LOC705596", "LOC702961", "LOC704054", "LOC715668", "LOC717801", "LOC707085", "LOC114679603", "LOC106999518", "LOC718267", "LOC705327", "LOC106992281", "LOC695218", "LOC702957", "LOC708147", "LOC719947", "LOC701392", "LOC699166", "LOC106999718", "LOC702760", "LOC702328", "LOC704267", "LOC719289", "LOC106997304", "LOC100423207", "LOC100428069", "LOC106999080", "LOC100427696", "LOC712160", "LOC712267", "LOC100425072", "LOC100427254", "LOC696068", "LOC694967", "LOC708492", "LOC710583", "LOC717763", "LOC693820", "LOC114678655", "LOC114678366", "LOC114678384", "LOC114671497", "LOC114675033", "LOC697719", "LOC694071", "LOC695523", "LOC703455", "LOC715814", "LOC106998837", "LOC713060", "LOC693904", "LOC711043", "LOC709241", "LOC693584", "LOC698301", "LOC703631", "LOC701292", "LOC706910", "LOC712630", "LOC714801", "LOC717838", "LOC698099", "LOC694067", "LOC706082", "LOC702514", "LOC711324", "LOC703616", "LOC704396", "LOC712274", "LOC698273", "LOC718556", "LOC715043", "LOC696015", "LOC698297", "LOC700262", "LOC695670", "LOC698383", "LOC708603", "LOC701421", "LOC697065", "LOC114677128", "LOC714656", "LOC106996346", "LOC703683", "LOC701691", "LOC698792", "LOC107000151", "LOC697561", "LOC710477", "LOC100427278", "LOC720748", "LOC114672187", "LOC708140", "LOC698768", "LOC716735", "LOC114673268", "LOC114674609", "LOC114674676", "LOC114674882", "LOC114675055", "LOC114675456", "LOC114674615", "LOC114674626", "LOC114674635", "LOC114674636", "LOC114674637", "LOC114674638", "LOC114674640", "LOC114674642", "LOC114674650", "LOC114674666", "LOC114674683", "LOC114673870", "LOC114675629", "LOC114675635", "LOC114675637", "LOC114675638", "LOC114675641", "LOC114675642", "LOC114675643", "LOC114675636", "LOC114675644", "LOC114675630", "LOC114675633", "LOC114675631", "LOC114675632", "LOC114675739", "LOC114675743", "LOC114675745", "LOC114675746", "LOC114675747", "LOC114675740", "LOC114675741", "LOC114675856", "LOC114675854", "LOC114675853", "LOC114675857", "LOC114675858", "LOC114675859", "LOC114675860", "LOC114675913", "LOC114675919", "LOC114675922", "LOC114675923", "LOC114675924", "LOC114675925", "LOC114675914", "LOC114675915", "LOC114675916", "LOC114675918", "LOC114675141", "LOC718979", "LOC106993215", "LOC106995250", "LOC709583", "LOC114679608", "LOC717779", "LOC707414", "LOC709376", "LOC710038", "LOC706793", "LOC106999723", "LOC696958", "LOC106993579", "LOC106995074", "LOC694799", "LOC106995394", "LOC698530", "LOC107000213", "LOC705400", "LOC720019", "LOC698143", "LOC697585", "LOC713714", "LOC702620", "LOC715037", "LOC699544", "LOC100427498", "LOC699681", "LOC701302", "LOC700008", "LOC698713", "LOC702871", "LOC693856", "LOC701386", "LOC716126", "LOC696423", "LOC114669857", "LOC697476", "LOC100429843", "LOC696901", "LOC693272", "LOC704083", "LOC702723", "LOC703433", "LOC722545", "LOC696877", "LOC106998431", "LOC106999185", "LOC706492", "LOC699695", "LOC713984", "LOC703435", "LOC709778", "LOC694122", "LOC711449", "LOC701763", "LOC719242", "LOC715711", "LOC700872", "LOC717246", "LOC698182", "LOC701156", "LOC106996680", "LOC710859", "LOC106997591", "LOC707834", "LOC100428649", "LOC695340", "LOC718357", "LOC702542", "LOC718020", "LOC699687", "LOC711174", "LOC709462", "LOC712987", "LOC106995957", "LOC708800", "LOC717286", "LOC698999", "LOC696145", "LOC106999371", "LOC698377", "LOC709045", "LOC711760", "LOC114680233", "LOC107000909", "LOC106994077", "LOC701710", "LOC114674062", "LOC699398", "LOC693578", "LOC106992566", "LOC106997285", "LOC718737", "LOC706606", "LOC704012", "LOC702297", "LOC114680376", "LOC696154", "LOC721751", "LOC704238", "LOC709820", "LOC114676029", "LOC708995", "LOC710502", "LOC695715", "LOC698942", "LOC696134", "LOC696785", "LOC698684", "LOC695740", "LOC706177", "LOC717053", "LOC698197", "LOC714598", "LOC106998794", "LOC704510", "LOC698130", "LOC107000483", "LOC716320", "LOC106994271", "LOC708074", "LOC100425638", "LOC709201", "LOC707358", "LOC706712", "LOC701457", "LOC114676221", "LOC114677736", "LOC100423145", "LOC708782", "LOC714171", "LOC707437", "LOC701466", "LOC719029", "LOC697987", "LOC714120", "LOC708085", "LOC694937", "LOC106993116", "LOC706340", "LOC697214", "LOC106995063", "LOC699344", "LOC114676734", "LOC702875", "LOC695122", "LOC717674", "LOC712555", "LOC711491", "LOC702677", "LOC704365", "LOC708118", "LOC709678", "LOC106994904", "LOC703784", "LOC702847", "LOC709086", "LOC114674318", "LOC693848", "LOC719244", "LOC114680572", "LOC719770", "LOC710317", "LOC714620", "LOC703648", "LOC703365", "LOC706181", "LOC700425", "LOC708644", "LOC709650", "LOC705067", "LOC713497", "LOC106994132", "LOC703919", "LOC114671097", "LOC703853", "LOC114674108", "LOC114676998", "LOC712599", "LOC114678374", "LOC114678397", "LOC114679023", "LOC699392", "LOC114678167", "LOC694228", "LOC710665", "LOC107000401", "LOC100423661", "LOC106999480", "LOC106997918", "LOC107000809", "LOC114673683", "LOC106998280", "LOC106998813", "LOC100429752", "LOC100423423", "LOC106994361", "LOC106994914", "LOC705174", "LOC707072", "LOC700862", "LOC693472", "LOC106998156", "LOC721192", "LOC707117", "LOC705979", "LOC705677", "LOC710287", "LOC704345", "LOC699239", "LOC702116", "LOC706754", "LOC703797", "LOC710877", "LOC696151", "LOC702932", "LOC695743", "LOC693287", "LOC703024", "LOC698657", "LOC100429815", "LOC707342", "LOC695463", "LOC699805", "LOC722113", "LOC694734", "LOC106998116", "LOC716075", "LOC703563", "LOC713469", "LOC714185", "LOC703251", "LOC703283", "LOC698417", "LOC704062", "LOC698226", "LOC114677434", "LOC693480", "LOC114676944", "LOC702978", "LOC100427953", "LOC100427759", "LOC704256", "LOC700045", "LOC702525", "LOC710595", "LOC698574", "LOC707182", "LOC700578", "LOC698448", "LOC709444", "LOC698086", "LOC714855", "LOC708405", "LOC114675505", "LOC697178", "LOC703216", "LOC716530", "LOC716150", "LOC694093", "LOC718478", "LOC707861", "LOC106998326", "LOC695279", "LOC106995044", "LOC100423364", "LOC100423295", "LOC704394", "LOC703794", "LOC693573", "LOC699375", "LOC701250", "LOC706496", "LOC693947", "LOC713991", "LOC710642", "LOC109910387", "LOC109910386", "LOC106997745", "LOC714700", "LOC100426636", "LOC106998409")) -.RegisterGeneSet("MMul10_Ribosomal", ribosomalGenes) +RegisterGeneSet("MMul10_Ribosomal", ribosomalGenes) # Identified by grep on the descriptions of all LOC* genes for 'mitochond' mitochondrialGenes <- c("LOC703370", "LOC721815", "LOC720015", "LOC703345", "LOC708979", "LOC704978", "LOC717349", "LOC718596", "LOC705988", "LOC703571", "LOC100429589", "LOC114672439", "LOC711644", "LOC705840", "LOC697510", "LOC100426562", "LOC100430397", "LOC705494", "LOC718356", "LOC708673", "LOC708221", "LOC693728", "LOC701224", "LOC695949", "LOC716130", "LOC100430580", "LOC100423136", "LOC106998857", "LOC701346", "LOC695671", "LOC696244", "LOC100427705", "LOC114673694", "LOC106997368", "LOC107000220", "LOC696031", "LOC708562", "LOC716946", "LOC715928", "LOC713542", "LOC719688", "LOC699117", "LOC694182", "LOC696890", "LOC707114", "LOC704076", "LOC704440", "LOC709495", "LOC702581", "LOC711636", "LOC698075", "LOC711183", "LOC698715", "LOC694260", "LOC707476", "LOC700815", "LOC711417", "LOC706691", "LOC696144", "LOC695041", "LOC701131", "LOC114676443", "LOC712886", "LOC114669858", "LOC106996230", "LOC701964", "LOC705178", "LOC700087", "LOC695277", "LOC695732", "LOC114678889", "LOC106995294", "LOC100425230", "LOC100425700", "LOC697409", "LOC710274", "LOC707227", "LOC701661", "LOC696956", "LOC106996920", "LOC701236", "LOC106992283", "LOC717879", "LOC114674848", "LOC106998783", "LOC106998836", "LOC114678228", "LOC114673956", "LOC114677410", "LOC114678786", "LOC114679364", "LOC114679428", "LOC114680400", "LOC114671073", "LOC100423866", "LOC106993150", "LOC106996000", "LOC107000216", "LOC699137", "LOC106996051", "LOC713467", "LOC114675539", "LOC693843", "LOC697678", "LOC702427", "LOC114675509", "LOC698520", "LOC106997494", "LOC100425012", "LOC106999579", "LOC107000931", "LOC106997075", "LOC717923", "LOC106998133", "LOC712330", "LOC706686", "LOC715327", "LOC693799", "LOC693766", "LOC698522", "LOC114675319", "LOC718745", "LOC718390", "LOC114678805", "LOC706366", "LOC114674124", "LOC106996824", "LOC106994877", "LOC106992611", "LOC107000653", "LOC107000976", "LOC713028", "LOC693813", "LOC711899", "LOC718711", "LOC114669720", "LOC721639", "LOC698302", "LOC718712", "LOC698305", "LOC706710", "LOC705282", "LOC114670386", "LOC699779", "LOC100427337", "LOC100429934", "LOC704917", "LOC715730", "LOC705066", "LOC709894", "LOC711634", "LOC723069", "LOC705183", "LOC702309", "LOC701966", "LOC704336", "LOC697416", "LOC106993325", "LOC716730", "LOC717607", "LOC106997886", "LOC107000665", "LOC106999488", "LOC106998010", "LOC705476", "LOC114673096", "LOC696696", "LOC715179") -.RegisterGeneSet("MMul10_Mitochondrial", mitochondrialGenes) +RegisterGeneSet("MMul10_Mitochondrial", mitochondrialGenes) igHeavyVariable <- c("LOC715358", "LOC114669771", "LOC106999620", "LOC106999619", "LOC114679735", "LOC114679700", "LOC114679702", "LOC114679730", "LOC114679696", "LOC106999621", "LOC114679699", "LOC721017", "LOC106995637", "LOC721043", "LOC721139", "LOC114679710", "LOC715165", "LOC720899", "LOC714894", "LOC106999623", "LOC106999617", "LOC714310", "LOC723533", "LOC715400", "LOC701407", "LOC720918", "LOC106999616", "LOC721119", "LOC114679704", "LOC715260", "LOC719378", "LOC106999631", "LOC721089", "LOC106999608", "LOC721132", "LOC720890", "LOC106999629", "LOC114679692", "LOC100430012", "LOC106999615", "LOC114669802", "LOC114679711", "LOC714939", "LOC715543", "LOC106999624", "LOC721104", "LOC114679713", "LOC721116", "LOC114679694", "LOC114679729", "LOC106999604", "LOC715594", "LOC106995900", "LOC106999610", "LOC106999609", "LOC721083", "LOC106999633", "LOC106996003", "LOC114679703", "LOC721002", "LOC106999628", "LOC114679693", "LOC722278", "LOC720985", "LOC720452", "LOC720904", "LOC114679728", "LOC114679707", "LOC720935", "LOC721108", "LOC720974", "LOC106999618", "LOC114679733", "LOC715733", "LOC114679736", "LOC714419") igKappaVariable <- c("LOC106993058", "LOC721353", "LOC703375", "LOC701600", "LOC701068", "LOC106993063", "LOC707007", "LOC709162", "LOC709703", "LOC709066", "LOC106993071", "LOC709793", "LOC707181", "LOC106993142", "LOC106992444", "LOC106993055", "LOC703139", "LOC114671809", "LOC106993143", "LOC723660", "LOC703610", "LOC106993056", "LOC114671797", "LOC708976", "LOC106993144", "LOC106998680", "LOC106993140", "LOC106993064", "LOC106993141", "LOC706869", "LOC707609", "LOC708249", "LOC709890", "LOC106993048", "LOC700696") igLambdaVariable <-c("LOC107000570", "LOC106992425", "LOC701976", "LOC708547", "LOC107000578", "LOC114670549", "LOC107000585", "LOC107000586", "LOC107000581", "LOC114670550", "LOC107000576", "LOC107000577", "LOC702421", "LOC701772", "LOC107000579", "LOC701240") -.RegisterGeneSet('MMul10_Ig_Variable', unique(c(igHeavyVariable, igKappaVariable, igLambdaVariable))) +RegisterGeneSet('MMul10_Ig_Variable', unique(c(igHeavyVariable, igKappaVariable, igLambdaVariable))) ## Human gene sets # Generated using: sort(rownames(seuratObj[['RNA']])[grepl(rownames(seuratObj[['RNA']]), pattern = '^RP[SL]')]) humanRibosomalGenes <- read.table(system.file("extdata/humanRibosomalGenes_Human_GRCh38_p13_Ensembl.tsv", package = "RIRA"), header = T)$ribosomal_genes -.RegisterGeneSet("HumanRibosomalGenes", humanRibosomalGenes) +RegisterGeneSet("HumanRibosomalGenes", humanRibosomalGenes) # Generated using: sort(rownames(seuratObj[["RNA"]])[grepl(rownames(seuratObj[["RNA"]]), pattern = '^MT-')]) humanMitochondrialGenes <- c('MT-ATP6','MT-ATP8','MT-CO1','MT-CO2','MT-CO3','MT-CYB','MT-ND1','MT-ND2','MT-ND3','MT-ND4','MT-ND4L','MT-ND5','MT-ND6','MT-RNR1','MT-RNR2','MT-TA','MT-TC','MT-TD','MT-TE','MT-TF','MT-TG','MT-TH','MT-TI','MT-TK','MT-TL1','MT-TL2','MT-TM','MT-TN','MT-TP','MT-TQ','MT-TR','MT-TS1','MT-TS2','MT-TT','MT-TV','MT-TW','MT-TY') -.RegisterGeneSet("HumanMitochondrialGenes", humanMitochondrialGenes) +RegisterGeneSet("HumanMitochondrialGenes", humanMitochondrialGenes) humanTravGenes <- c('TRAV1-1','TRAV1-2','TRAV10','TRAV11','TRAV12-1','TRAV12-2','TRAV12-3','TRAV13-1','TRAV13-2','TRAV14DV4','TRAV15','TRAV16','TRAV17','TRAV18','TRAV19','TRAV2','TRAV20','TRAV21','TRAV22','TRAV23DV6','TRAV24','TRAV25','TRAV26-1','TRAV26-2','TRAV27','TRAV28','TRAV29DV5','TRAV3','TRAV30','TRAV31','TRAV32','TRAV33','TRAV34','TRAV35','TRAV36DV7','TRAV37','TRAV38-1','TRAV38-2DV8','TRAV39','TRAV4','TRAV40','TRAV41','TRAV5','TRAV6','TRAV7','TRAV8-1','TRAV8-2','TRAV8-3','TRAV8-4','TRAV8-5','TRAV8-6','TRAV8-7','TRAV9-1','TRAV9-2') humanTrbvGenes <- c('TRBV1','TRBV10-1','TRBV10-2','TRBV10-3','TRBV11-1','TRBV11-2','TRBV11-3','TRBV12-1','TRBV12-2','TRBV12-3','TRBV12-4','TRBV12-5','TRBV13','TRBV14','TRBV15','TRBV16','TRBV17','TRBV18','TRBV19','TRBV2','TRBV20-1','TRBV20OR9-2','TRBV21-1','TRBV21OR9-2','TRBV22-1','TRBV22OR9-2','TRBV23-1','TRBV23OR9-2','TRBV24-1','TRBV24OR9-2','TRBV25-1','TRBV25OR9-2','TRBV26','TRBV26OR9-2','TRBV27','TRBV28','TRBV29-1','TRBV29OR9-2','TRBV3-1','TRBV30','TRBV4-1','TRBV4-2','TRBV5-1','TRBV5-2','TRBV5-3','TRBV5-4','TRBV5-5','TRBV5-6','TRBV5-7','TRBV6-1','TRBV6-2','TRBV6-4','TRBV6-5','TRBV6-6','TRBV6-7','TRBV6-8','TRBV7-1','TRBV7-2','TRBV7-3','TRBV7-4','TRBV7-5','TRBV7-6','TRBV7-7','TRBV7-9','TRBV8-1','TRBV8-2','TRBV9','TRBVA','TRBVB') humanTrbdGenes <- c('TRBD1') humanTrajGenes <- c('TRAJ1','TRAJ10','TRAJ11','TRAJ12','TRAJ13','TRAJ14','TRAJ16','TRAJ17','TRAJ18','TRAJ19','TRAJ2','TRAJ20','TRAJ21','TRAJ22','TRAJ23','TRAJ24','TRAJ25','TRAJ26','TRAJ27','TRAJ28','TRAJ29','TRAJ3','TRAJ30','TRAJ31','TRAJ32','TRAJ33','TRAJ34','TRAJ35','TRAJ36','TRAJ37','TRAJ38','TRAJ39','TRAJ4','TRAJ40','TRAJ41','TRAJ42','TRAJ43','TRAJ44','TRAJ45','TRAJ46','TRAJ47','TRAJ48','TRAJ49','TRAJ5','TRAJ50','TRAJ51','TRAJ52','TRAJ53','TRAJ54','TRAJ55','TRAJ56','TRAJ57','TRAJ58','TRAJ59','TRAJ6','TRAJ60','TRAJ61','TRAJ7','TRAJ8','TRAJ9') humanTrbjGenes <- c('TRBJ1-1','TRBJ1-2','TRBJ1-3','TRBJ1-4','TRBJ1-5','TRBJ1-6','TRBJ2-1','TRBJ2-2','TRBJ2-2P','TRBJ2-3','TRBJ2-4','TRBJ2-5','TRBJ2-6','TRBJ2-7') -.RegisterGeneSet("HumanTcrGenes", c(humanTravGenes, humanTrbvGenes, humanTrajGenes, humanTrbjGenes, humanTrbdGenes)) +RegisterGeneSet("HumanTcrGenes", c(humanTravGenes, humanTrbvGenes, humanTrajGenes, humanTrbjGenes, humanTrbdGenes)) # Generated via sort(rownames(seuratObj[["RNA"]])[grepl(rownames(seuratObj[["RNA"]]), pattern = '^IGHV')]). humanIgHeavyVariable <- c('IGHV1-12','IGHV1-14','IGHV1-17','IGHV1-18','IGHV1-2','IGHV1-24','IGHV1-3','IGHV1-45','IGHV1-46','IGHV1-58','IGHV1-67','IGHV1-68','IGHV1-69','IGHV1-69-2','IGHV1-69D','IGHV1OR15-1','IGHV1OR15-2','IGHV1OR15-3','IGHV1OR15-4','IGHV1OR15-6','IGHV1OR15-9','IGHV1OR16-1','IGHV1OR16-2','IGHV1OR16-3','IGHV1OR16-4','IGHV1OR21-1','IGHV2-26','IGHV2-5','IGHV2-70','IGHV2-70D','IGHV2OR16-5','IGHV3-11','IGHV3-13','IGHV3-15','IGHV3-16','IGHV3-19','IGHV3-20','IGHV3-21','IGHV3-22','IGHV3-23','IGHV3-25','IGHV3-29','IGHV3-30','IGHV3-30-2','IGHV3-32','IGHV3-33','IGHV3-33-2','IGHV3-35','IGHV3-36','IGHV3-37','IGHV3-38','IGHV3-41','IGHV3-42','IGHV3-43','IGHV3-47','IGHV3-48','IGHV3-49','IGHV3-50','IGHV3-52','IGHV3-53','IGHV3-54','IGHV3-57','IGHV3-6','IGHV3-60','IGHV3-62','IGHV3-63','IGHV3-64','IGHV3-64D','IGHV3-65','IGHV3-66','IGHV3-69-1','IGHV3-7','IGHV3-71','IGHV3-72','IGHV3-73','IGHV3-74','IGHV3-75','IGHV3-76','IGHV3-79','IGHV3OR15-7','IGHV3OR16-10','IGHV3OR16-11','IGHV3OR16-12','IGHV3OR16-13','IGHV3OR16-15','IGHV3OR16-16','IGHV3OR16-17','IGHV3OR16-6','IGHV3OR16-7','IGHV3OR16-8','IGHV3OR16-9','IGHV4-28','IGHV4-31','IGHV4-34','IGHV4-39','IGHV4-4','IGHV4-55','IGHV4-59','IGHV4-61','IGHV4-80','IGHV4OR15-8','IGHV5-10-1','IGHV5-51','IGHV5-78','IGHV6-1','IGHV7-27','IGHV7-34-1','IGHV7-4-1','IGHV7-40','IGHV7-56','IGHV7-81','IGHV8-51-1','IGHVII-1-1','IGHVII-15-1','IGHVII-22-1','IGHVII-26-2','IGHVII-28-1','IGHVII-30-1','IGHVII-30-21','IGHVII-33-1','IGHVII-40-1','IGHVII-43-1','IGHVII-44-2','IGHVII-46-1','IGHVII-49-1','IGHVII-51-2','IGHVII-53-1','IGHVII-60-1','IGHVII-62-1','IGHVII-65-1','IGHVII-67-1','IGHVII-74-1','IGHVII-78-1','IGHVIII-11-1','IGHVIII-13-1','IGHVIII-16-1','IGHVIII-2-1','IGHVIII-22-2','IGHVIII-25-1','IGHVIII-26-1','IGHVIII-38-1','IGHVIII-44','IGHVIII-47-1','IGHVIII-5-1','IGHVIII-5-2','IGHVIII-67-2','IGHVIII-67-3','IGHVIII-67-4','IGHVIII-76-1','IGHVIII-82','IGHVIV-44-1') @@ -455,16 +463,16 @@ humanIgHeavyDiversity <- c('IGHD','IGHD1-1','IGHD1-14','IGHD1-20','IGHD1-26','IG humanIgLambda <- c('IGLJ1','IGLJ2','IGLJ3','IGLJ4','IGLJ5','IGLJ6','IGLJ7','IGLJCOR18','IGLL1','IGLL3P','IGLL4P','IGLL5','IGLON5','IGLV1-36','IGLV1-40','IGLV1-41','IGLV1-44','IGLV1-47','IGLV1-50','IGLV1-51','IGLV1-62','IGLV10-54','IGLV10-67','IGLV11-55','IGLV2-11','IGLV2-14','IGLV2-18','IGLV2-23','IGLV2-28','IGLV2-33','IGLV2-34','IGLV2-5','IGLV2-8','IGLV3-1','IGLV3-10','IGLV3-12','IGLV3-13','IGLV3-15','IGLV3-16','IGLV3-17','IGLV3-19','IGLV3-2','IGLV3-21','IGLV3-22','IGLV3-24','IGLV3-25','IGLV3-26','IGLV3-27','IGLV3-29','IGLV3-30','IGLV3-31','IGLV3-32','IGLV3-4','IGLV3-6','IGLV3-7','IGLV3-9','IGLV4-3','IGLV4-60','IGLV4-69','IGLV5-37','IGLV5-45','IGLV5-48','IGLV5-52','IGLV6-57','IGLV7-35','IGLV7-43','IGLV7-46','IGLV8-61','IGLV8OR8-1','IGLV9-49','IGLVI-20','IGLVI-38','IGLVI-42','IGLVI-56','IGLVI-63','IGLVI-68','IGLVI-70','IGLVIV-53','IGLVIV-59','IGLVIV-64','IGLVIV-65','IGLVIV-66-1','IGLVIVOR22-1','IGLVIVOR22-2','IGLVV-58','IGLVV-66','IGLVVI-22-1','IGLVVI-25-1','IGLVVII-41-1') # Generated via sort(rownames(seuratObj[["RNA"]])[grepl(rownames(seuratObj[["RNA"]]), pattern = '^IGK')]). I excluded IGKC genes to conserve the constant chain expression. humanIgKappa <- c('IGKJ1','IGKJ2','IGKJ3','IGKJ4','IGKJ5','IGKV1-12','IGKV1-13','IGKV1-16','IGKV1-17','IGKV1-22','IGKV1-27','IGKV1-32','IGKV1-33','IGKV1-35','IGKV1-37','IGKV1-39','IGKV1-5','IGKV1-6','IGKV1-8','IGKV1-9','IGKV1D-12','IGKV1D-13','IGKV1D-16','IGKV1D-17','IGKV1D-22','IGKV1D-27','IGKV1D-32','IGKV1D-33','IGKV1D-35','IGKV1D-37','IGKV1D-39','IGKV1D-42','IGKV1D-43','IGKV1D-8','IGKV1OR-2','IGKV1OR-3','IGKV1OR1-1','IGKV1OR10-1','IGKV1OR2-1','IGKV1OR2-108','IGKV1OR2-11','IGKV1OR2-118','IGKV1OR2-2','IGKV1OR2-3','IGKV1OR2-6','IGKV1OR2-9','IGKV1OR22-1','IGKV1OR22-5','IGKV1OR9-1','IGKV1OR9-2','IGKV2-10','IGKV2-14','IGKV2-18','IGKV2-19','IGKV2-23','IGKV2-24','IGKV2-26','IGKV2-28','IGKV2-29','IGKV2-30','IGKV2-36','IGKV2-38','IGKV2-4','IGKV2-40','IGKV2D-10','IGKV2D-14','IGKV2D-18','IGKV2D-19','IGKV2D-23','IGKV2D-24','IGKV2D-26','IGKV2D-28','IGKV2D-29','IGKV2D-30','IGKV2D-36','IGKV2D-38','IGKV2D-40','IGKV2OR2-1','IGKV2OR2-10','IGKV2OR2-2','IGKV2OR2-7','IGKV2OR2-7D','IGKV2OR2-8','IGKV2OR22-3','IGKV2OR22-4','IGKV3-11','IGKV3-15','IGKV3-20','IGKV3-25','IGKV3-31','IGKV3-34','IGKV3-7','IGKV3D-11','IGKV3D-15','IGKV3D-20','IGKV3D-25','IGKV3D-31','IGKV3D-34','IGKV3D-7','IGKV3OR2-268','IGKV3OR2-5','IGKV3OR22-2','IGKV4-1','IGKV5-2','IGKV6-21','IGKV6D-21','IGKV6D-41','IGKV7-3') -.RegisterGeneSet("HumanBcrGenes", c(humanIgHeavyVariable, humanIgHeavyJoining, humanIgHeavyDiversity, humanIgLambda, humanIgKappa)) +RegisterGeneSet("HumanBcrGenes", c(humanIgHeavyVariable, humanIgHeavyJoining, humanIgHeavyDiversity, humanIgLambda, humanIgKappa)) # Generated via sort(rownames(seuratObj[["RNA"]])[grepl(rownames(seuratObj[["RNA"]]), pattern = '^KIR)]). humanKIRGenes <- c('KIR2DL1','KIR2DL3','KIR2DL4','KIR2DP1','KIR2DS4','KIR3DL1','KIR3DL2','KIR3DL3','KIR3DP1','KIR3DX1','KIRREL1','KIRREL1-IT1','KIRREL2','KIRREL3','KIRREL3-AS1','KIRREL3-AS2','KIRREL3-AS3') -.RegisterGeneSet("HumanKIRGenes", humanKIRGenes) +RegisterGeneSet("HumanKIRGenes", humanKIRGenes) # Generated via sort(rownames(seuratObj[["RNA"]])[grepl(rownames(seuratObj[["RNA"]]), pattern = '^HLA-[^D]')]). humanHLAGenes <- c('HLA-A','HLA-B','HLA-C','HLA-E','HLA-F','HLA-F-AS1','HLA-G','HLA-H','HLA-J','HLA-K','HLA-L','HLA-L.1','HLA-N','HLA-P','HLA-S','HLA-T','HLA-U','HLA-V','HLA-V.1','HLA-W','HLA-Z') -.RegisterGeneSet("HumanHLAGenes", humanHLAGenes) +RegisterGeneSet("HumanHLAGenes", humanHLAGenes) # NOTE: this has been deprecated in favor of .2, which omits TCR constant region -.RegisterGeneSet('VariableGenes_Exclusion.1', unique(c( +RegisterGeneSet('VariableGenes_Exclusion.1', unique(c( GetGeneSet('MMul10TcrGenes'), GetGeneSet('MMul10TcrConstantRegion'), GetGeneSet('MMul10_MHC'), @@ -474,7 +482,7 @@ humanHLAGenes <- c('HLA-A','HLA-B','HLA-C','HLA-E','HLA-F','HLA-F-AS1','HLA-G', GetGeneSet('MMul10_Ig_Variable') ))) -.RegisterGeneSet('VariableGenes_Exclusion.2', unique(c( +RegisterGeneSet('VariableGenes_Exclusion.2', unique(c( GetGeneSet('MMul10TcrGenes'), GetGeneSet('MMul10_MHC'), GetGeneSet('MMul10_KIR'), @@ -483,7 +491,7 @@ humanHLAGenes <- c('HLA-A','HLA-B','HLA-C','HLA-E','HLA-F','HLA-F-AS1','HLA-G', GetGeneSet('MMul10_Ig_Variable') ))) -.RegisterGeneSet('HumanVariableGenes_Exclusion', unique(c( +RegisterGeneSet('HumanVariableGenes_Exclusion', unique(c( GetGeneSet('HumanMitochondrialGenes'), GetGeneSet('HumanRibosomalGenes'), GetGeneSet('HumanTcrGenes'), @@ -492,27 +500,27 @@ humanHLAGenes <- c('HLA-A','HLA-B','HLA-C','HLA-E','HLA-F','HLA-F-AS1','HLA-G', GetGeneSet('HumanHLAGenes') ))) -.RegisterGeneSet("Glycolysis", c("ALDOA", "BPGM", "ENO1", "ENO2", "GAPDH", "HK1", "HK2", "HKDC1", "PFKL", "PGAM1", "PGAM2", "PGK1", "PKLR", "PKM", "TPI1")) -.RegisterGeneSet('Interferon_Response', c('IFI6','IFI27','MX1','ISG15','STAT1','LOC114672189','MX2','IFIT3')) -.RegisterGeneSet('Interferon_Response_IFI6_correlated', c('IFI6', 'ISG15', 'MX1', 'RNF213', 'BST2', 'DDX60', 'MX2', 'LOC100427967', 'STAT1', 'OAS2', 'DHX58', 'LY6E-1', 'IFIT3', 'SP100', 'EPSTI1')) +RegisterGeneSet("Glycolysis", c("ALDOA", "BPGM", "ENO1", "ENO2", "GAPDH", "HK1", "HK2", "HKDC1", "PFKL", "PGAM1", "PGAM2", "PGK1", "PKLR", "PKM", "TPI1")) +RegisterGeneSet('Interferon_Response', c('IFI6','IFI27','MX1','ISG15','STAT1','LOC114672189','MX2','IFIT3')) +RegisterGeneSet('Interferon_Response_IFI6_correlated', c('IFI6', 'ISG15', 'MX1', 'RNF213', 'BST2', 'DDX60', 'MX2', 'LOC100427967', 'STAT1', 'OAS2', 'DHX58', 'LY6E-1', 'IFIT3', 'SP100', 'EPSTI1')) -.RegisterGeneSet('MHC-II', c('IFI30', 'CD74', 'MAMU-DRB1', 'MAMU-DRA', 'MAMU-DQA1','MAMU-DRB5','CST3')) +RegisterGeneSet('MHC-II', c('IFI30', 'CD74', 'MAMU-DRB1', 'MAMU-DRA', 'MAMU-DQA1','MAMU-DRB5','CST3')) # Lists provided by Rebecca Skalsky. NOTE: CD24, CD27 and CEACAM21 not annotated in MMul10 -.RegisterGeneSet('B cells', c('MS4A1', 'CD79A', 'CD79B')) -.RegisterGeneSet('Follicular B cells', c('CD19', 'MS4A1', 'CR2', 'CD22', 'FCER2', 'CXCR5', 'MAMU-DRA', 'PAX5')) # Also 'CD24' -.RegisterGeneSet('Activated B cell', c('CD19', 'CD69', 'MS4A1', 'IL2RA', 'CD86', 'FLT3', 'PAX5', 'BACH2', 'IRF4')) # Also CD27 -.RegisterGeneSet('Germinal Center B cell', c('CD38', 'CD37', 'FCER2')) # Also CD27 -.RegisterGeneSet('Dark zone (centroblast)', c('CD38', 'CXCR4', 'A4GALT', 'AICDA', 'FOXO1', 'MKI67', 'CDK1', 'CCND3', 'PAX5', 'BCL6', 'MEF2B')) -.RegisterGeneSet('Light zone (centrocyte)', c('CD38', 'CXCR5', 'CD83', 'BATF', 'BCL2A1')) -.RegisterGeneSet('Memory B cell precursor in LZ', c('CCR6', 'GPR183', 'PLAC8', 'MAML2', 'IL23A')) -.RegisterGeneSet('Memory B cells', c('CD19', 'MS4A1', 'CR2', 'CD40', 'CD80', 'CD86', 'MAMU-DRA', 'POU2AF1', 'PAX5')) # Also CEACAM21, CD27 -.RegisterGeneSet('Plasma cell', c('SDC1', 'CD38', 'TNFRSF17', 'CXCR4', 'TNFRSF17', 'PRDM1', 'IRF4', 'XBP1')) # Also CD27 -.RegisterGeneSet('Short-lived plasmablast', c('CD19', 'CD38', 'TNFRSF17', 'CXCR4')) # Also CD27 -.RegisterGeneSet('Marginal Zone B cells (spleen)', c('CD19', 'MS4A1', 'CR2', 'FCER2', 'FCRL3', 'CD1C', 'EBF1', 'TCF3', 'PAX5')) # Also CD27 +RegisterGeneSet('B cells', c('MS4A1', 'CD79A', 'CD79B')) +RegisterGeneSet('Follicular B cells', c('CD19', 'MS4A1', 'CR2', 'CD22', 'FCER2', 'CXCR5', 'MAMU-DRA', 'PAX5')) # Also 'CD24' +RegisterGeneSet('Activated B cell', c('CD19', 'CD69', 'MS4A1', 'IL2RA', 'CD86', 'FLT3', 'PAX5', 'BACH2', 'IRF4')) # Also CD27 +RegisterGeneSet('Germinal Center B cell', c('CD38', 'CD37', 'FCER2')) # Also CD27 +RegisterGeneSet('Dark zone (centroblast)', c('CD38', 'CXCR4', 'A4GALT', 'AICDA', 'FOXO1', 'MKI67', 'CDK1', 'CCND3', 'PAX5', 'BCL6', 'MEF2B')) +RegisterGeneSet('Light zone (centrocyte)', c('CD38', 'CXCR5', 'CD83', 'BATF', 'BCL2A1')) +RegisterGeneSet('Memory B cell precursor in LZ', c('CCR6', 'GPR183', 'PLAC8', 'MAML2', 'IL23A')) +RegisterGeneSet('Memory B cells', c('CD19', 'MS4A1', 'CR2', 'CD40', 'CD80', 'CD86', 'MAMU-DRA', 'POU2AF1', 'PAX5')) # Also CEACAM21, CD27 +RegisterGeneSet('Plasma cell', c('SDC1', 'CD38', 'TNFRSF17', 'CXCR4', 'TNFRSF17', 'PRDM1', 'IRF4', 'XBP1')) # Also CD27 +RegisterGeneSet('Short-lived plasmablast', c('CD19', 'CD38', 'TNFRSF17', 'CXCR4')) # Also CD27 +RegisterGeneSet('Marginal Zone B cells (spleen)', c('CD19', 'MS4A1', 'CR2', 'FCER2', 'FCRL3', 'CD1C', 'EBF1', 'TCF3', 'PAX5')) # Also CD27 # SLC2A1 = Glut-1, SLC3A2 = CD98 -.RegisterGeneSet('Redox', c('SLC2A1', 'SLC3A2')) +RegisterGeneSet('Redox', c('SLC2A1', 'SLC3A2')) # https://www.nature.com/articles/s41590-021-00898-1: # ATP*: ATPase @@ -521,11 +529,11 @@ humanHLAGenes <- c('HLA-A','HLA-B','HLA-C','HLA-E','HLA-F','HLA-F-AS1','HLA-G', # UQCR*: Mitochondrial respiratory chain # KEGG, OXPHOS gene set -.RegisterGeneSet('Metabolism', c('NLRX1', 'FASTKD5', 'GLUT1', 'GLUT2', 'FASTDK5')) +RegisterGeneSet('Metabolism', c('NLRX1', 'FASTKD5', 'GLUT1', 'GLUT2', 'FASTDK5')) -.RegisterGeneSet('InflMyeloid', c('CCL3','LOC100426537','LOC114673087','LOC100423954','CCL4L1','LOC100426632','LOC100430627','TNF','TNFAIP3','PTX3','IL1B','NLRP3','CXCL3','CXCL8','PMAIP1')) +RegisterGeneSet('InflMyeloid', c('CCL3','LOC100426537','LOC114673087','LOC100423954','CCL4L1','LOC100426632','LOC100430627','TNF','TNFAIP3','PTX3','IL1B','NLRP3','CXCL3','CXCL8','PMAIP1')) -.RegisterGeneSet('TNK_MaybeExhaustion', c('TNFAIP3','TOX','STAT4','ITK','BCL2','TGFBR2','PTPRC','ITGA4','RORA', 'RUNX1')) +RegisterGeneSet('TNK_MaybeExhaustion', c('TNFAIP3','TOX','STAT4','ITK','BCL2','TGFBR2','PTPRC','ITGA4','RORA', 'RUNX1')) #' @title GetMMul10TcrGenes #' @param includeConstantRegion If true, the MMul10TcrConstantRegion GeneSet will be included. @@ -608,7 +616,7 @@ ExpandGeneList <- function(genes, verbose = TRUE) { #' @param seuratObj A Seurat Object storing the count matrix to be used for phenotyping. #' @param yField The grouping variable used to calculate the average expression of genes and the y axis of the DotPlot. #' @param scaled A boolean defining whether to color dots by scaled expression or unscaled expression. -#' @param gene_lists A vector of gene lists (defined by .RegisterGeneSet) to be queried and their genes be plotted. +#' @param gene_lists A vector of gene lists (defined by RegisterGeneSet) to be queried and their genes be plotted. #' @param scale.by Allow different scaling methods for dot size. 'radius' will de-emphasize lower/intermediately percent expressed genes. #' @param assay Which assay to use in the input seuratObj #' @export diff --git a/man/MakePhenotypingDotPlot.Rd b/man/MakePhenotypingDotPlot.Rd index 030a31d..138544b 100644 --- a/man/MakePhenotypingDotPlot.Rd +++ b/man/MakePhenotypingDotPlot.Rd @@ -20,7 +20,7 @@ MakePhenotypingDotPlot( \item{scaled}{A boolean defining whether to color dots by scaled expression or unscaled expression.} -\item{gene_lists}{A vector of gene lists (defined by .RegisterGeneSet) to be queried and their genes be plotted.} +\item{gene_lists}{A vector of gene lists (defined by RegisterGeneSet) to be queried and their genes be plotted.} \item{assay}{Which assay to use in the input seuratObj} diff --git a/man/RegisterGeneSet.Rd b/man/RegisterGeneSet.Rd new file mode 100644 index 0000000..06dc6d0 --- /dev/null +++ b/man/RegisterGeneSet.Rd @@ -0,0 +1,16 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/Phenotyping.R +\name{RegisterGeneSet} +\alias{RegisterGeneSet} +\title{RegisterGeneSet} +\usage{ +RegisterGeneSet(name, genes) +} +\arguments{ +\item{name}{The name of the gene set} + +\item{genes}{A character vector of gene names} +} +\description{ +Registers a named gene set in the package gene-set registry. +}