readSignedGmt: Read signed GMT files

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

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")

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