Label clusters in clustered gene sets list object

Label clusters in clustered gene sets list object

Usage

labelClusters(
  geneSetsList,
  stopWords = geneSetSimplifyR::stopWords,
  nLabels = 10,
  removeFirstWord = FALSE,
  verbose = TRUE
)

Arguments

geneSetsList

'gsList' object that has been clustered with the 'clusterGeneSets()' function.

stopWords

Vector with stop words. The default vector can be viewed with data(stopWords). To add new stop words 'stopWords <- c(geneSetSimplifyR::stopWords, 'new word 1', 'new word 2', ...)

nLabels

Number of top labels to keep. Default to 10

removeFirstWord

Logical. If TRUE, strip the first word (everything before the first underscore) from each gene-set name before generating bigram tokens. Useful for MSigDB-style names where the first token is an author or database prefix (e.g. "GOBP", "GOMF", "HALLMARK"). Default: FALSE.

verbose

a logic indicating whether to print progress statements. Defaults to TRUE.

Value

'gsList' object with labeled clusters for all clustered resolutions.

Examples

# Relabel the shipped example, e.g. with extra stop words
gsListObject <- labelClusters(
  geneSetsList = exampleGsList,
  stopWords = c(stopWords, "regulation"),
  verbose = FALSE
)