quantileNormalisation: Step 8: Apply Beta-Mixture Quantile normalisation, producing...

In NeilPearson-Lilly/MethyLiution: MethyLiution: A QC Pipeline For Methylation Data

Description

This probably isn't something you want to run directly. Just use the runPipeline() function.

Usage

quantileNormalisation(begin, mset_file, logfile, BMIQ_dir, outdir, threads,
  col.name = NULL, mset.lumi = NULL, meth.B = NULL)

Arguments

begin	Step the pipeline begins at
mset_file	Path to file in which dataset object is stored between steps (auto-filled by runPipeline() function)
logfile	Path to log file (auto-filled by runPipeline() function)
BMIQ_dir	Path to a directory where BMIQ normalised data can be written to files (auto-filled by runPipeline() function)
outdir	Path to output directory
threads	Number of threads to run certain tasks in parallel
col.name	List of column names, generated by setColumnNames() (auto-filled by runPipeline() function)
mset.lumi	Microarray dataset object (auto-filled by runPipeline() function)
meth.B	Object containing normalised data, made during Step 7. (auto-filled by runPipeline() function)

Value

list - mset.lumi dataset, BMIQ-normalised data object (B values), BMIQ-normalised data object (M-values)

NeilPearson-Lilly/MethyLiution documentation built on May 21, 2019, 11:29 a.m.