meffil.plot.probe.batch: Test normalized betas for association with known batch...

In perishky/meffil: Efficient algorithms for DNA methylation

Test normalized betas for association with known batch variables

Description

Performs association of each of n PCs calculated from most variable CpG sites (after normalization) against each of m measured batch variables

Usage

meffil.plot.probe.batch(
  norm.objects,
  pcs,
  variables = guess.batch.vars(norm.objects),
  additional = NULL,
  batch.threshold = 1e-50,
  cols = NULL,
  verbose = T
)

Arguments

norm.objects	Output from meffil.normalize.quantiles().
pcs	Output from meffil.methylation.pcs() applied to the normalized methylation matrix corresponding to norm.objects.
variables	Default = guess.batch.vars(norm). Which variables in sample sheet to test
additional.	Default = NULL. Data frame containing variables to test for association with control matrix PCs. Must have nrow(additional) == length(norm.objects).
verbose=T	Print progress messages?

Value

List of table of results and graph

perishky/meffil documentation built on March 20, 2024, 1:56 a.m.