R: A single-array preprocessing method for estimating...

doCRMAv2 {aroma.affymetrix}

R Documentation

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

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).

Value

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

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(s)

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.