meffil.qc.summary: Perform QC analysis on idat files

In perishky/meffil: Efficient algorithms for DNA methylation

Perform QC analysis on idat files

Description

Performs a number of QC analyses including checking for sex differences, methylated vs unmethylated levels, deviation from control probe means, detection p-values and bead numbers per sample and probe.

Usage

meffil.qc.summary(
  qc.objects,
  genotypes = NULL,
  parameters = meffil.qc.parameters(),
  verbose = TRUE
)

Arguments

qc.objects	From meffil.qc
genotypes	Optional output from meffil.extract.genotypes(). Sample genotypes are matched to sample qc.objects using colnames(genotypes) and names(qc.objects).
parameters	Default = meffil.qc.parameters(). List of parameter values. See meffil.qc.parameters

Details

Also returns list of sample IDs and CPGs that are low quality.

Value

List

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