readIdatFiles: Reads Idat Files from Infinium II Illumina BeadChips

In benilton/crlmm-release: Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays.

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?

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.

Value

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

Author(s)

Matt Ritchie

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

#RG = readIdatFiles()

benilton/crlmm-release documentation built on May 12, 2019, 10:59 a.m.