methylumiR {methylumi} | R Documentation

## 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()`

### Details

Used to construct a MethyLumiSet object....

### Value

A MethyLumiSet object

### Author(s)

Sean Davis <sdavis2@mail.nih.gov>

### See Also

`MethyLumiSet-class`, `MethyLumiQC-class`

### Examples

    ## 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

[Package methylumi version 2.35.0 Index]