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]