crlmmIllumina: Genotype Illumina Infinium II BeadChip data with CRLMM

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

Description

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

Usage

crlmmIllumina(RG, XY, 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=0.7)

Arguments

RG	NChannelSet containing R and G bead intensities
XY	NChannelSet containing X and Y bead intensities
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)

Details

Note: The user should specify either the RG or XY intensities, not both.

Value

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.

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.

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.

Examples

## crlmmOut = crlmmIllumina(RG)

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