normalisation: Step 7: Apply inter-assay normalisation Apply a broader...

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

normalisation(begin, mset_file, logfile, normalisation_method, outdir,
  col.name = NULL, mset.lumi = NULL, lumi.C = NULL,
  sub_assays = 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)
normalisation_method	Normalisation method: one of 'quantile', 'ssn', or 'none'.
outdir	Path to output directory
col.name	List of column names, generated by setColumnNames() (auto-filled by runPipeline() function)
mset.lumi	Microarray dataset object (auto-filled by runPipeline() function)
lumi.C	Colour-balanced dataset object (auto-filled by runPipeline() function)
sub_assays	Object containing breakdown of sub-assays, made during Step 5. (auto-filled by runPipeline() function)

Value

list - mset.lumi dataset, meth.B normalised dataset object (exprs), meth.M normalised dataset object (betas)

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