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

View source: R/normalization-report.r

meffil.normalization.summaryR Documentation

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 June 9, 2024, 5:59 p.m.