findSurrogateVariables: Step 10: Apply surrogate variable analysis to automatically...

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

findSurrogateVariables(begin, mset_file, sv_file, logfile,
  col.name = NULL, mset.lumi = NULL, bmiq.M = 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)
sv_file	Path to file where any surrogate variables found are written as output (auto-filled by runPipeline() function)
logfile	Path to log file (auto-filled by runPipeline() function)
col.name	List of column names, generated by setColumnNames() (auto-filled by runPipeline() function)
mset.lumi	Microarray dataset object (auto-filled by runPipeline() function)
bmiq.M	Object containing BMIQ-normalised data, made during Step 8. (auto-filled by runPipeline() function)

Value

mset.lumi dataset

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