Compute word frequencies for a single MSigDB collection
computeMsigWordFreq( msigGsc, weight = NULL, measure = c("tfidf", "tf"), version = msigdb::getMsigdbVersions(), org = c("auto", "hs", "mm"), rmwords = getMsigBlacklist() )
a GeneSetCollection object, containing gene sets from the
GSEABase::getBroadSets() function can be used to parse XML
files downloaded from MSigDB.
a named numeric vector, containing weights to apply to each gene-set. This can be -log10(FDR), -log10(p-value) or an enrichment score (ideally unsigned).
a character, specifying how frequencies should be computed. "tf" uses term frequencies and "tfidf" (default) applies inverse document frequency weights to term frequencies.
a character, specifying the version of msigdb to use (see
a character, specifying the organism to use. This can either be "auto" (default), "hs" or "mm".
a character vector, containing a blacklist of words to discard from the analysis.
a list, containing two data.frames summarising the results of the frequency analysis on gene set names and short descriptions.
data(hgsc) freq <- computeMsigWordFreq(hgsc, measure = 'tfidf') #> Warning: Assuming the organism to be human.