gmtlist2signedGenesets: Convert gmtlist into a list of signed genesets

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

Description

Convert gmtlist into a list of signed genesets

Usage

gmtlist2signedGenesets(
  gmtlist,
  posPattern = "_UP$",
  negPattern = "_DN$",
  nomatch = c("ignore", "pos", "neg")
)

Arguments

gmtlist	A gmtlist object, probably read-in by readGmt
posPattern	Regular expression pattern of positive gene sets. It is trimmed from the original name to get the stem name of the gene set. See examples below.
negPattern	Regular expression pattern of negative gene sets. It is trimmed from the original name to get the stem name of the gene set. See examples below.
nomatch	Options to deal with gene sets that match neither positive nor negative patterns. ignore: they will be ignored (but not discarded, see details below); pos: they will be counted as positive signs; neg: they will be counted as negative signs

Value

An S4-object of SignedGenesets, which is a list of signed_geneset, each being a two-item list; the first item is 'pos', containing a character vector of positive genes; and the second item is 'neg', containing a character vector of negative genes.

Gene set names are detected whether they are positive or negative. If neither positive nor negative, nomatch will determine how will they be interpreted. In case of pos (or neg), such genesets will be treated as positive (or negative) gene sets.In case nomatch is set to ignore, the gene set will appear in the returned values with both positive and negative sets set to NULL.

Examples

testInputList <- list(list(name="GeneSetA_UP",genes=LETTERS[1:3]),
               list(name="GeneSetA_DN", genes=LETTERS[4:6]),
               list(name="GeneSetB", genes=LETTERS[2:4]),
               list(name="GeneSetC_DN", genes=LETTERS[1:3]),
               list(name="GeneSetD_UP", genes=LETTERS[1:3]))
testOutputList.ignore <- gmtlist2signedGenesets(testInputList, nomatch="ignore")
testOutputList.pos <- gmtlist2signedGenesets(testInputList, nomatch="pos")
testOutputList.neg <- gmtlist2signedGenesets(testInputList, nomatch="neg")

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