read_Illu_meth450k: Reading methylation data from Illumina array...

Description Usage Arguments Details Value Note Author(s)

View source: R/MT_read_Illu_meth450k.R

Description

Create an RGChannelSet object from Illumina IDAT files and add phenotype data.

Usage

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read_Illu_meth450k(baseDir, SampleSheetRegExp = ".csv",
  sampleColumn = "Sample_Name", covarfile = NULL, covarsampleID = "ID")

Arguments

baseDir

character with path to base directory containing IDAT files for all arrays.

SampleSheetRegExp

dataframe with sample sheet or character with regular expression for identifying the corresponding sample sheet within the base directory or its subdirectories. If NULL, no sample information file is loaded.

sampleColumn

Name of sample column in sample sheet

covarfile

character with filepath to a covariates file if given. NULL otherwise.

covarsampleID

character with name of sample column in (optional) covariates file.

Details

This functions uses the minfi package to load methylation data from Illumnia Human Methylation 450k microarrays. If the SampleSheetRegExp argument is NULL, the function finds all two-color IDAT files in the directory given by baseDir including all subdirectories. Two-color IDAT files consist of pairs of files with names ending in _Red.idat or _Grn.idat. If SampleSheetRegExp is not NULL, the corresponding sample sheet is identified via regular expression (file must be located in base) and all listed arrays are loaded. Susequently, additional phenotype data given in covarfile is added to the object.

Value

RGChannelSet object

Note

methylation data classes (from minfi manual) :

Author(s)

Frank Ruehle


frankRuehle/systemsbio documentation built on July 3, 2018, 10:05 a.m.