methylumiR: Load data from Illumina methylation platform

Description

This function is useful for loading Illumina methylation data into a MethyLumiSet object. Sample information can be supplied and will then be incorporated into the resulting phenoData slot.

Usage

methylumiR(filename, qcfile=NULL, sampleDescriptions = NULL, sep = NULL, ...)

Arguments

filename

A filename of the excel-like file from BeadStudio

qcfile

A filename of the excel-like file from BeadStudio

sampleDescriptions

A data.frame that contains at least one column, SampleID (case insensitive). This column MUST match the part of the column headers before the .Avg_Beta, etc. Also, if a column called SampleLabel (case insensitive), it is used for sample labels, IF the sampleLabel column contains unique identifiers

sep

seperator used in the BeadStudio (or GenomeStudio) output file. If it is NULL, the function will automatically estimate it.

...

Passed into read.delim()

Value

A MethyLumiSet object

Details

Used to construct a MethyLumiSet object....

Examples

Run this code

## Read in sample information
samps <- read.table(system.file("extdata/samples.txt",
                                package = "methylumi"),sep="t",header=TRUE)
## Perform the actual data reading
## This is an example of reading data from an 
## Sentrix Array format file (actually two files,
## one for data and one for QC probes)
mldat <- methylumiR(system.file('extdata/exampledata.samples.txt',package='methylumi'),
                    qcfile=system.file('extdata/exampledata.controls.txt',package="methylumi"),
                    sampleDescriptions=samps)
mldat

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