globalStats: Test for global methylation differences

In ben-laufer/DMRichR: Enrich your DMR Analysis with the Tidyverse

Test for global methylation differences

Description

Computes the average smoothed global CpG methylation values for each sample and tests for differences between groups while adjusting for the provided covariates. CpG island testing is performed for the human, mouse, and rat genomes. Global methylation and CpG island differences are tested for using an ANOVA through the aov function.

Usage

globalStats(
  bs.filtered.bsseq = bs.filtered.bsseq,
  genome = genome,
  testCovariate = testCovariate,
  adjustCovariate = NULL,
  matchCovariate = NULL
)

Arguments

bs.filtered.bsseq	Smoothed bsseq object with design matrix in pData
genome	Character specifying the genome of interest
testCovariate	The factor to test for differences between groups
adjustCovariate	The covariate(s) to adjust for between groups
matchCovariate	Another covariate to adjust for between groups (for dmrseq compatibility)

Details

globalStats

Value

A list of tibbles with smoothed global and CpG island methylation statistics and the values used for the tests

ben-laufer/DMRichR documentation built on Oct. 1, 2023, 7:25 a.m.