Test for global methylation differences

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)

Value

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

Details

globalStats