meffil.normalization.summary: Perform tests to check normalization performance

In perishky/meffil: Efficient algorithms for DNA methylation

Perform tests to check normalization performance

Description

Creates scree plot of PCs of control probes, tests for association of control probe PCs with batch variables, tests for association of normalized probes with batch variables, creates PCA plots

Usage

meffil.normalization.summary(
  norm.objects,
  pcs,
  parameters = meffil.normalization.parameters(norm.objects),
  variables = NULL,
  verbose = TRUE
)

Arguments

norm.objects	Output from meffil.normalize.quantiles
pcs	Output from meffil.methylation.pcs() applied to the normalized methylation matrix corresponding to norm.objects.
parameters	Default = meffil.post.parameters(norm.objects). Report parameters.
variables	Default = NULL. Data frame of variables to compare to principal components (pcs). Must contain length(norm.objects) rows. Columns that are not factors are ignored.
verbose	Default = TRUE

Value

List of tables and graphs.

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