computeMsigWordFreq {vissE} | R Documentation

## Compute word frequencies for a single MSigDB collection

### Description

Compute word frequencies for a single MSigDB collection

### Usage

    computeMsigWordFreq(
      msigGsc,
      weight = NULL,
      measure = c("tfidf", "tf"),
      version = msigdb::getMsigdbVersions(),
      org = c("auto", "hs", "mm"),
      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.
`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 `msigdb::getMsigdbVersions()`).
`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.

### 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 1.2.2 Index]