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crlmm (version 1.30.0)

readIdatFiles: Reads Idat Files from Infinium II Illumina BeadChips

Description

Reads intensity information for each bead type from .idat files of Infinium II genotyping BeadChips

Usage

readIdatFiles(sampleSheet=NULL, arrayNames=NULL, ids=NULL, path="", arrayInfoColNames=list(barcode="SentrixBarcode_A", position="SentrixPosition_A"), highDensity=FALSE, sep="_", fileExt=list(green="Grn.idat", red="Red.idat"), saveDate=FALSE, verbose=FALSE)

Arguments

sampleSheet
data.frame containing Illumina sample sheet information (for required columns, refer to BeadStudio Genotyping guide - Appendix A).
arrayNames
character vector containing names of arrays to be read in. If NULL, all arrays that can be found in the specified working directory will be read in.
ids
vector containing ids of probes to be read in. If NULL all probes found on the first array are read in.
path
character string specifying the location of files to be read by the function
arrayInfoColNames
(used when sampleSheet is specified) list containing elements 'barcode' which indicates column names in the sampleSheet which contains the arrayNumber/barcode number and 'position' which indicates the strip number. In older style sample sheets, this information is combined (usually in a column named 'SentrixPosition') and this should be specified as list(barcode=NULL, position="SentrixPosition")
highDensity
logical (used when sampleSheet is specified). If TRUE, array extensions '\_A', '\_B' in sampleSheet are replaced with 'R01C01', 'R01C02' etc.
sep
character string specifying separator used in .idat file names.
fileExt
list containing elements 'Green' and 'Red' which specify the .idat file extension for the Cy3 and Cy5 channels.
saveDate
logical. Should the dates from each .idat be saved with sample information?
verbose
logical. Should processing information be displayed as data is read in?

Value

NChannelSet with intensity data (R, G), and indicator for SNPs with 0 beads (zero) for each bead type.

Details

The summarised Cy3 (G) and Cy5 (R) intensities (on the orginal scale) are read in from the .idat files.

Where available, a sampleSheet data.frame, in the same format as used by BeadStudio (columns 'Sample\_ID', 'SentrixBarcode\_A' and 'SentrixPosition\_A' are required) which keeps track of sample information can be specified.

Thanks to Keith Baggerly who provided the code to read in the binary .idat files.

References

Ritchie ME, Carvalho BS, Hetrick KN, Tavar\'e S, Irizarry RA. R/Bioconductor software for Illumina's Infinium whole-genome genotyping BeadChips. Bioinformatics. 2009 Oct 1;25(19):2621-3.

Examples

Run this code

#RG = readIdatFiles()

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