doCRMAv1 | R Documentation |
Estimation and assessment of raw copy numbers at the single locus level (CRMA v1) 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.
## S3 method for class 'AffymetrixCelSet'
doCRMAv1(csR, shift=+300, combineAlleles=TRUE, lengthRange=NULL, arrays=NULL, drop=TRUE,
verbose=FALSE, ...)
## Default S3 method:
doCRMAv1(dataSet, ..., verbose=FALSE)
## Default S3 method:
doASCRMAv1(...)
csR , dataSet |
An |
shift |
An tuning parameter specifying how much to shift the probe signals before probe summarization. |
combineAlleles |
A |
lengthRange |
An optional |
arrays |
A |
drop |
If |
verbose |
See |
... |
Additional arguments used to set up |
Returns a named list
, iff drop == FALSE
, otherwise
only ChipEffectSet
object.
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
.
doASCRMAv1(...)
is a wrapper for
doCRMAv1(..., combineAlleles=FALSE)
.
Henrik Bengtsson
[1] H. Bengtsson, R. Irizarry, B. Carvalho & T.P. Speed.
Estimation and assessment of raw copy numbers at the
single locus level,
Bioinformatics, 2008.
For CRMA v2 (recommended by authors), which is a single-array
improvement over CRMA v1, see doCRMAv2
().
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