computeMsigWordFreq {vissE} | R Documentation |
Compute word frequencies for a single MSigDB collection
computeMsigWordFreq( msigGsc, measure = c("tfidf", "tf"), rmwords = getMsigBlacklist() )
msigGsc |
a GeneSetCollection object, containing gene sets from the
MSigDB. The |
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. |
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')