methylumiR: Load data from Illumina methylation platform
In methylumi: Handle Illumina methylation data

Description Usage Arguments Details Value Author(s) See Also Examples

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.

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

`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()`

Used to construct a MethyLumiSet object....

A MethyLumiSet object

Sean Davis <sdavis2@mail.nih.gov>

MethyLumiSet-class, MethyLumiQC-class

## 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