computeMsigWordFreq {vissE} | R Documentation |
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() )
msigGsc |
a GeneSetCollection object, containing gene sets from the
MSigDB. The |
weight |
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). |
measure |
a character, specifying how frequencies should be computed. "tf" uses term frequencies and "tfidf" (default) applies inverse document frequency weights to term frequencies. |
version |
a character, specifying the version of msigdb to use (see
|
org |
a character, specifying the organism to use. This can either be "auto" (default), "hs" or "mm". |
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')