methylumiR {methylumi} | R Documentation |
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.
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 |
sep |
seperator used in the BeadStudio (or GenomeStudio) output file. If it is NULL, the function will automatically estimate it. |
... |
Passed into |
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