meffil.plot.control.batch: Test for association of control matrix probes with known...

In perishky/meffil: Efficient algorithms for DNA methylation

Test for association of control matrix probes with known batch variables

Description

Performs association of each of n PCs calculated from the control matrix against each of m measured batch variables

Usage

meffil.plot.control.batch(
  norm.objects,
  npcs = 1:10,
  variables = guess.batch.vars(norm.objects),
  additional = NULL,
  batch.threshold = 1e-50,
  cols = NULL,
  verbose = TRUE
)

Arguments

norm.objects	From meffil.normalize.quantiles
pcs	Which PCs to plot. Default first 10
variables.	Default = guess.batch.vars(norm.objects). Array spacifying column names in samplesheet to test for association with control matrix PCs.
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

Data frame of results plus plot

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