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 1.15.4 Index]