computeMsigWordFreq: Compute word frequencies for a single MSigDB collection

In DavisLaboratory/enrichnets: Visualising Set Enrichment Analysis Results

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 = getMsigExclusionList(),
  idf = NULL
)

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 an exclusion list of words to discard from the analysis.
idf	a list of named numeric vectors, specifying inverse document frequencies to use to penalise terms from gene-set names and short descriptions. This should be a vector of length 2 with names "Name" and "Short". Numeric vectors should contain weights and names should represent the term. Precomputed versions can be retrieved using the msigdb::getMsigdbIDF().

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')

DavisLaboratory/enrichnets documentation built on Feb. 2, 2024, 9:14 a.m.