matchGenes: Match genes in a list-like object to a vector of genesymbols

In BioQC: Detect tissue heterogeneity in expression profiles with gene sets

Description

Match genes in a list-like object to a vector of genesymbols

Usage

matchGenes(list, object, ...)

## S4 method for signature 'GmtList,character'
matchGenes(list, object)

## S4 method for signature 'GmtList,matrix'
matchGenes(list, object)

## S4 method for signature 'GmtList,eSet'
matchGenes(list, object, col = "GeneSymbol")

## S4 method for signature 'character,character'
matchGenes(list, object)

## S4 method for signature 'character,matrix'
matchGenes(list, object)

## S4 method for signature 'character,eSet'
matchGenes(list, object)

## S4 method for signature 'character,DGEList'
matchGenes(list, object, col = "GeneSymbol")

## S4 method for signature 'GmtList,DGEList'
matchGenes(list, object, col = "GeneSymbol")

## S4 method for signature 'SignedGenesets,character'
matchGenes(list, object)

## S4 method for signature 'SignedGenesets,matrix'
matchGenes(list, object)

## S4 method for signature 'SignedGenesets,eSet'
matchGenes(list, object, col = "GeneSymbol")

## S4 method for signature 'SignedGenesets,DGEList'
matchGenes(list, object, col = "GeneSymbol")

Arguments

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 eSet object.
...	additional arguments like col
col	Column name of fData in an eSet object, or genes in an DGEList object, to specify where gene symbols are stored. The default value is set to "GeneSymbol"

Value

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.

Examples

## 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)

## 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)

## 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)
## force using row names
matchGenes(testGeneSets, testEset, col=NULL)

 ## 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")
 }

## test character, character
matchGenes(c("gene1", "gene2"), testGenes)

## test character, matrix
matchGenes(c("gene1", "gene2"), testGeneExprs)

## test character, eset
matchGenes(c("gene1", "gene2"), testEset)

BioQC documentation built on Nov. 8, 2020, 7:16 p.m.