overRepresentationAnalysis: Over-representation analysis

Description Usage Arguments Value

View source: R/over_representation_analysis.R

Description

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

Usage

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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


martingarrido/biokit documentation built on June 27, 2021, 2:21 a.m.