matchGenes {BioQC} | R Documentation

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

### 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)

[Package BioQC version 1.18.0 Index]