doCRMAv2: A single-array preprocessing method for estimating full-resolution raw copy numbers from all Affymetrix genotyping arrays (CRMA v2)

Description

A single-array preprocessing method for estimating full-resolution raw copy numbers from all Affymetrix genotyping arrays (CRMA v2) based on [1]. The algorithm is processed in bounded memory, meaning virtually any number of arrays can be analyzed on also very limited computer systems.

We recommend CRMA v2 for estimating allele-specific as well total SNP signals from Affymetrix SNP chips.

Usage

# S3 method for AffymetrixCelSet
doCRMAv2(csR, combineAlleles=TRUE, lengthRange=NULL, arrays=NULL,
  plm=c("AvgCnPlm", "RmaCnPlm"), drop=TRUE, verbose=FALSE, ...)
  # S3 method for default
doCRMAv2(dataSet, ..., verbose=FALSE)
  # S3 method for default
doASCRMAv2(...)

Value

Returns a named list, iff drop == FALSE, otherwise only ChipEffectSet object.

Arguments

csR, dataSet: An AffymetrixCelSet (or the name of an AffymetrixCelSet).
combineAlleles: A logical specifying whether allele probe pairs should be summed before modeling or not.
lengthRange: An optional numeric vector of length two passed to FragmentLengthNormalization.
arrays: A integer vector specifying the subset of arrays to process. If NULL, all arrays are considered.
plm: A character string specifying which type of probe-summarization model to used.
drop: If TRUE, the summaries are returned, otherwise a named list of all intermediate and final results.
verbose: See Verbose.
...: Additional arguments used to set up AffymetrixCelSet (when argument dataSet is specified).

Allele-specific or only total-SNP signals

If you wish to obtain allele-specific estimates for SNPs, which are needed to call genotypes or infer parent-specific copy numbers, then use argument combineAlleles=FALSE. Total copy number signals are still available. If you know for certain that you will not use allele-specific estimates, you will get slightly less noisy signals (very small difference) if you use combineAlleles=TRUE.

doASCRMAv2(...) is a wrapper for doCRMAv2(..., combineAlleles=FALSE).

Author

Henrik Bengtsson

References

[1] H. Bengtsson, P. Wirapati & T.P. Speed. A single-array preprocessing method for estimating full-resolution raw copy numbers from all Affymetrix genotyping arrays including GenomeWideSNP 5 & 6, Bioinformatics, 2009.