overRepresentationAnalysis: Over-representation analysis
In martingarridorc/biokit: Toolkit for the automatic analysis of omics data

View source: R/over_representation_analysis.R

Uses two different approaches to assess the significance of the over-representation of a feature vector over a list of functional categories. Uses fisherExactTest.

overRepresentationAnalysis(
  features,
  funCatList,
  universe,
  minSize = 1,
  maxSize = Inf,
  removeNoOverlap = TRUE,
  pAdjustMethod = "BH"
)

`features`	A vecor of characters that contains the features to analyze.
`funCatList`	A list of character vectors with the functional categories to analyze.
`universe`	A vector of characters to be used as the statistical background for the different tests. If not supplied, defaults to all the features in funCatList.
`minSize`	Minimal size of a functional category to test. All functional categories below the threshold are excluded.
`maxSize`	Minimal size of a functional category to test. All functional categories aboce the threshold are excluded.
`removeNoOverlap`	Remove functional categories without overlapping features before performing the P adjustment?
`pAdjustMethod`	The method used to correct estimated p values. Passed to p.adjust.