crlmmIlluminaV2: Read and Genotype Illumina Infinium II BeadChip data with...
In benilton/crlmm-release: Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays.

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

Implementation of the CRLMM algorithm for data from Illumina's Infinium II BeadChips.

crlmmIlluminaV2(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, stripNorm=TRUE, useTarget=TRUE,
      row.names=TRUE, col.names=TRUE, probs=c(1/3, 1/3, 1/3),
      DF=6, SNRMin=5, gender=NULL, seed=1, mixtureSampleSize=10^5,
      eps=0.1, verbose=TRUE, cdfName, sns, recallMin=10,
      recallRegMin=1000, returnParams=FALSE, badSNP=.7)

`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?
`stripNorm`	'logical'. Should the data be strip-level normalized?
`useTarget`	'logical' (only used when `stripNorm=TRUE`). Should the reference HapMap intensities be used in strip-level normalization?
`row.names`	'logical'. Use rownames - SNP names?
`col.names`	'logical'. Use colnames - Sample names?
`probs`	'numeric' vector with priors for AA, AB and BB.
`DF`	'integer' with number of degrees of freedom to use with t-distribution.
`SNRMin`	'numeric' scalar defining the minimum SNR used to filter out samples.
`gender`	'integer' vector, with same length as 'filenames', defining sex. (1 - male; 2 - female)
`seed`	'integer' scalar for random number generator (used to sample `mixtureSampleSize` SNPs for mixture model.
`mixtureSampleSize`	'integer'. The number of SNP's to be used when fitting the mixture model.
`eps`	Minimum change for mixture model.
`verbose`	'logical'.
`cdfName`	'character' defining the chip annotation (manifest) to use ('human370v1c', human550v3b', 'human650v3a', 'human1mv1c', 'human370quadv3c', 'human610quadv1b', 'human660quadv1a', 'human1mduov3b', 'humanomni1quadv1b', 'humanomniexpress12v1b', 'humancytosnp12v2p1h')
`sns`	'character' vector with sample names to be used.
`recallMin`	'integer'. Minimum number of samples for recalibration.
`recallRegMin`	'integer'. Minimum number of SNP's for regression.
`returnParams`	'logical'. Return recalibrated parameters.
`badSNP`	'numeric'. Threshold to flag as bad SNP (affects batchQC)

This function combines the reading of data from idat files using readIdatFiles and genotyping to reduce memory usage.

A SnpSet object which contains

`calls`	Genotype calls (1 - AA, 2 - AB, 3 - BB)
`callProbability`	confidence scores 'round(-1000*log2(1-p))'

in the assayData slot and

`SNPQC`	SNP Quality Scores
`batchQC`	Batch Quality Scores

along with center and scale parameters when returnParams=TRUE in the featureData slot.

Matt Ritchie

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.

Carvalho B, Bengtsson H, Speed TP, Irizarry RA. Exploration, normalization, and genotype calls of high-density oligonucleotide SNP array data. Biostatistics. 2007 Apr;8(2):485-99. Epub 2006 Dec 22. PMID: 17189563.

Carvalho BS, Louis TA, Irizarry RA. Quantifying uncertainty in genotype calls. Bioinformatics. 2010 Jan 15;26(2):242-9.

crlmmIllumina

1 2	## crlmmOut = crlmmIlluminaV2(samples,path=path,arrayInfoColNames=list(barcode="Chip",position="Section"), ## saveDate=TRUE,cdfName="human370v1c",returnParams=TRUE)

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