removeSnpProbesAndImprintingGenes: Step 2: Filter SNP probes and imprinting genes

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

removeSnpProbesAndImprintingGenes(begin, mset_file, qc_probe_plot_file,
  logfile, array, col.name = NULL, mset.lumi = 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)
qc_probe_plot_file	Path to file where probe QC information will be written (auto-filled by runPipeline() function)
logfile	Path to log file (auto-filled by runPipeline() function)
array	Microarray probeset used: valid options are "450K" and "EPIC" (default "450K")
col.name	List of column names, generated by setColumnNames() (auto-filled by runPipeline() function)
mset.lumi	Microarray dataset object (auto-filled by runPipeline() function)

Value

mset.lumi dataset, with SNP probes and imprinting genes filtered out

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