readGenCallOutput: Read X and Y intensities from GenCall output

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

Description

This function reads the raw X and Y intensities output by GenomeStudio's GenCall genotyping module in preparation for genotyping with crlmm.

Usage

readGenCallOutput(filenames, path=".", cdfName, colnames=list("SampleID"="Sample ID", "SNPID"="SNP Name", "XRaw"="X Raw", "YRaw"="Y Raw"),
                  type=list("SampleID"="character", "SNPID"="character", "XRaw"="integer", "YRaw"="integer"), verbose=FALSE)

Arguments

filenames	'character' string, or a vector of character string specifying the name of the file(s) to read in
path	'character' string specifying the location of file to be read by the function
cdfName	'character' defining the chip annotation (manifest) to use ('human370v1c', human550v3b', 'human650v3a', 'human1mv1c', 'human370quadv3c', 'human610quadv1b', 'human660quadv1a', 'human1mduov3b', 'humanomni1quadv1b', 'humanomniexpress12v1b', 'humancytosnp12v2p1h')
colnames	list containing elements 'SampleID', 'SNPID', 'XRaw' and 'YRaw', which specify the column names from in 'file' that pertain to these variables. The default should suffice in most situations.
type	list containing data types for the columns to be read in. The default should be fine in most situations.
verbose	'logical'. Should processing information be displayed as data is read in?

Details

This function returns an NChannelSet containing raw intensity data (X and Y) from GenCall final report file. It assumes the GenCall output is formatted to have samples listed one below the other, and that the columns 'X Raw' and 'Y Raw' are available in the file. The function crlmmillumina() can be run on the output of the readGenCallOutput function.

Value

NChannelSet containing X and Y bead intensities.

Author(s)

Cynthia Liu, Matt Ritchie, Zhiyin Dai

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

#XY = readGenCallOutput(file="Hap650Yv3_Final_Report.txt", cdfName="human650v3a")
#crlmmOut = crlmmIllumina(XY=XY)

crlmm documentation built on Nov. 8, 2020, 4:55 p.m.