matchGenes.Rd
Match genes in a list-like object to a vector of genesymbols
matchGenes(list, object, ...) # S4 method for GmtList,character matchGenes(list, object) # S4 method for GmtList,matrix matchGenes(list, object) # S4 method for GmtList,eSet matchGenes(list, object, col = "GeneSymbol") # S4 method for character,character matchGenes(list, object) # S4 method for character,matrix matchGenes(list, object) # S4 method for character,eSet matchGenes(list, object) # S4 method for character,DGEList matchGenes(list, object, col = "GeneSymbol") # S4 method for GmtList,DGEList matchGenes(list, object, col = "GeneSymbol") # S4 method for SignedGenesets,character matchGenes(list, object) # S4 method for SignedGenesets,matrix matchGenes(list, object) # S4 method for SignedGenesets,eSet matchGenes(list, object, col = "GeneSymbol") # S4 method for SignedGenesets,DGEList matchGenes(list, object, col = "GeneSymbol")
list | A GmtList, list, character or SignedGenesets object |
---|---|
object | Gene symbols to be matched; they can come from a vector of character strings, or
a column in the fData of an |
... | additional arguments like |
col | Column name of |
An IndexList
object, which is essentially a list of the same length as input (length of 1
in case characters are used as input), with matching indices.
## test GmtList, character testGenes <- sprintf("gene%d", 1:10) testGeneSets <- GmtList(list(gs1=c("gene1", "gene2"), gs2=c("gene9", "gene10"), gs3=c("gene100"))) matchGenes(testGeneSets, testGenes)#> A list of 3 indices with offset=1 #> Options: NA removed: TRUE; duplicates removed: TRUE #> gs1 (n=2): 1,2 #> gs2 (n=2): 9,10 #> gs3 (n=0): NA## test GmtList, matrix testGenes <- sprintf("gene%d", 1:10) testGeneSets <- GmtList(list(gs1=c("gene1", "gene2"), gs2=c("gene9", "gene10"), gs3=c("gene100"))) testGeneExprs <- matrix(rnorm(100), nrow=10, dimnames=list(testGenes, sprintf("sample%d", 1:10))) matchGenes(testGeneSets, testGeneExprs)#> A list of 3 indices with offset=1 #> Options: NA removed: TRUE; duplicates removed: TRUE #> gs1 (n=2): 1,2 #> gs2 (n=2): 9,10 #> gs3 (n=0): NA## test GmtList, eSet testGenes <- sprintf("gene%d", 1:10) testGeneSets <- GmtList(list(gs1=c("gene1", "gene2"), gs2=c("gene9", "gene10"), gs3=c("gene100"))) testGeneExprs <- matrix(rnorm(100), nrow=10, dimnames=list(testGenes, sprintf("sample%d", 1:10))) testFeat <- data.frame(GeneSymbol=rownames(testGeneExprs), row.names=testGenes) testPheno <- data.frame(SampleId=colnames(testGeneExprs), row.names=colnames(testGeneExprs)) testEset <- ExpressionSet(assayData=testGeneExprs, featureData=AnnotatedDataFrame(testFeat), phenoData=AnnotatedDataFrame(testPheno)) matchGenes(testGeneSets, testGeneExprs)#> A list of 3 indices with offset=1 #> Options: NA removed: TRUE; duplicates removed: TRUE #> gs1 (n=2): 1,2 #> gs2 (n=2): 9,10 #> gs3 (n=0): NA## force using row names matchGenes(testGeneSets, testEset, col=NULL)#> A list of 3 indices with offset=1 #> Options: NA removed: TRUE; duplicates removed: TRUE #> gs1 (n=2): 1,2 #> gs2 (n=2): 9,10 #> gs3 (n=0): NA## test GmtList, DGEList if(requireNamespace("edgeR")) { mat <- matrix(rnbinom(100, mu=5, size=2), ncol=10) rownames(mat) <- sprintf("gene%d", 1:nrow(mat)) y <- edgeR::DGEList(counts=mat, group=rep(1:2, each=5)) ## if genes are not set, row names of the count matrix will be used for lookup myGeneSet <- GmtList(list(gs1=rownames(mat)[1:2], gs2=rownames(mat)[9:10], gs3="gene100")) matchGenes(myGeneSet, y) matchGenes(c("gene1", "gene2"), y) ## alternatively, use 'col' parameter to specify the column in 'genes' y2 <- edgeR::DGEList(counts=mat, group=rep(1:2, each=5), genes=data.frame(GeneIdentifier=rownames(mat), row.names=rownames(mat))) matchGenes(myGeneSet, y2, col="GeneIdentifier") }#> A list of 3 indices with offset=1 #> Options: NA removed: TRUE; duplicates removed: TRUE #> gs1 (n=2): 1,2 #> gs2 (n=2): 9,10 #> gs3 (n=0): NA#> A list of 1 indices with offset=1 #> Options: NA removed: TRUE; duplicates removed: TRUE #> TempGeneSet (n=2): 1,2#> A list of 1 indices with offset=1 #> Options: NA removed: TRUE; duplicates removed: TRUE #> TempGeneSet (n=2): 1,2#> A list of 1 indices with offset=1 #> Options: NA removed: TRUE; duplicates removed: TRUE #> TempGeneSet (n=2): 1,2