Over-representation analysis — overRepresentationAnalysis • biokit

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"
)

Arguments

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.

Value

A data frame with results in a tidy format