readSignedGmt {BioQC} | R Documentation

## Read signed GMT files

### Description

Read signed GMT files

### Usage

    readSignedGmt(
      filename,
      posPattern = "_UP$",
      negPattern = "_DN$",
      nomatch = c("ignore", "pos", "neg"),
      uniqGenes = TRUE,
      namespace = NULL
    )

### Arguments

`filename` | A gmt file
`posPattern` | Pattern of positive gene sets
`negPattern` | Pattern of negative gene sets
`nomatch` | options to deal with gene sets that match to neither posPattern nor negPattern patterns
`uniqGenes` | Logical, whether genes should be made unique
`namespace` | Character string or `NULL`, namespace of gene-sets

### See Also

`gmtlist2signedGenesets` for parameters `posPattern`, `negPattern`, and `nomatch`

### Examples

    testGmtFile <- system.file("extdata/test.gmt", package="BioQC")
    testSignedGenesets.ignore <- readSignedGmt(testGmtFile, nomatch="ignore")
    testSignedGenesets.pos <- readSignedGmt(testGmtFile, nomatch="pos")
    testSignedGenesets.neg <- readSignedGmt(testGmtFile, nomatch="neg")

[Package BioQC version 1.18.0 Index]