enrichmentTests: Tests for every function annotation in 'case.anno.tbl' the...

In asishallab/GeneFamilies: Analyses different properties of gene families

Tests for every function annotation in 'case.anno.tbl' the alternative hypothesis provided with 'test.dir'. Resulting p.values are adjusted for multiple hypothesis testing, before being returned. Note, if applied on large data sets, run in parallel on multiple cores and set options('mc.cores'=...) accordingly.

Description

Tests for every function annotation in 'case.anno.tbl' the alternative hypothesis provided with 'test.dir'. Resulting p.values are adjusted for multiple hypothesis testing, before being returned. Note, if applied on large data sets, run in parallel on multiple cores and set options('mc.cores'=...) accordingly.

Usage

enrichmentTests(case.anno.tbl, universe.anno.tbl, test.dir = "greater",
  p.adjust.method = "BY")

Arguments

case.anno.tbl	the annotations for which the alternative hypothesis is to be tested
universe.anno.tbl	the 'universe' annotations to compare the case with
test.dir	the direction of the alternative hypothesis. Default defines it as 'greater'
p.adjust.method	the method used to adjust resulting p.values for multiple hypothesis testing. Default is 'BY', see base::p.adjust for more details.

Value

A data.frame holding the annotation in column 'PFam', the adjusted and un-adjusted P.Value in two additional columns.

asishallab/GeneFamilies documentation built on May 22, 2023, 11:30 a.m.