qc_pipe: QC pipeline.

In markgene/yamat: Yet Another Methylation Array Toolkit

QC pipeline.

Description

QC pipeline.

Usage

qc_pipe(
  rgset,
  output,
  qc_csv = "qc.csv",
  qc_excel = "qc.xlsx",
  beta_value_distribution_file = "beta_value_histogram_fill_by_sample.png",
  background_offset = 3000,
  verbose = TRUE
)

Arguments

rgset	An object of RGChannelSet-class.
output	output directory.
qc_csv	QC metrics CSV file.
qc_excel	QC metrics Excel file.
beta_value_distribution_file	a plot file for beta value distribution.
background_offset	background correction offset. Default to 3000.
verbose	A logical scalar. Default to TRUE.

Value

An object of RGChannelSet-class with QC metrics added to phenotype data.

markgene/yamat documentation built on Aug. 26, 2024, 11:56 p.m.