read_Illu_meth450k: Reading methylation data from Illumina array...

In frankRuehle/systemsbio: Streamlined Analysis and Integration of Systems Biology Data

Description

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

Usage

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) :

• RGChannelSet: raw data from the IDAT files; this data is organized at the probe (not CpG locus) level. This data has two channels: Red and Green. This data type contains control probe data.

• MethylSet: data organized by the CpG locus level, but not mapped to a genome. This data has two channels: Meth (methylated) and Unmeth (unmethylated).

• RatioSet: data organized by the CpG locus level, but not mapped to a genome. The data has at least one of two channels: Beta and/or M (logratio of Beta). It may optionally include a CN channel (copy number).

• GenomicMethylSet: like a MethylSet, but mapped to a genome.

• GenomicRatioSet: like a RatioSet, but mapped to the genome.

Author(s)

Frank Ruehle

frankRuehle/systemsbio documentation built on Sept. 14, 2020, 1:18 a.m.