computeMsigWordFreq {vissE}R Documentation

Compute word frequencies for a single MSigDB collection

Description

Compute word frequencies for a single MSigDB collection

Usage

computeMsigWordFreq(
  msigGsc,
  measure = c("tfidf", "tf"),
  rmwords = getMsigBlacklist()
)

Arguments

msigGsc

a GeneSetCollection object, containing gene sets from the MSigDB. The GSEABase::getBroadSets() function can be used to parse XML files downloaded from MSigDB.

measure

a character, specifying how frequencies should be computed. "tf" uses term frequencies and "tfidf" (default) applies inverse document frequency weights to term frequencies.

rmwords

a character vector, containing a blacklist of words to discard from the analysis.

Value

a list, containing two data.frames summarising the results of the frequency analysis on gene set names and short descriptions.

Examples

data(hgsc)
freq <- computeMsigWordFreq(hgsc, measure = 'tfidf')


[Package vissE version 1.0.0 Index]