readSignedGmt: Read signed GMT files

Description Usage Arguments See Also Examples

View source: R/readGmt.R

Description

Read signed GMT files

Usage

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

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

See Also

gmtlist2signedGenesets for parameters posPattern, negPattern, and nomatch

Examples

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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 May 2, 2018, 3:40 a.m.