readSignedGmt {BioQC} | R Documentation |
Read signed GMT files
readSignedGmt( filename, posPattern = "_UP$", negPattern = "_DN$", nomatch = c("ignore", "pos", "neg"), uniqGenes = TRUE, namespace = NULL )
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 |
gmtlist2signedGenesets
for parameters posPattern
, negPattern
, and nomatch
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")