Description Usage Arguments Value Flavors References See Also Examples
Normalize allele-specific copy numbers (CA,CB).
1 2 3 |
data |
An Jx2xI |
references |
An index |
... |
Additional arguments passed to the internal fit function
|
truncate |
If |
refAvgFcn |
(optional) A |
flavor |
A |
verbose |
See |
Returns an Jx2xI numeric
array
with the same dimension names as argument data
.
For backward compatibility, we try to keep all major versions of
the CalMaTe algorithm available. Older versions can be used by
specifying argument flavor
.
The default flavor is v2
.
For more information about the different flavors,
see fitCalMaTeInternal
.
[1] M. Ortiz-Estevez, A. Aramburu, H. Bengtsson, P. Neuvial and A. Rubio, CalMaTe: A method and software to improve allele-specific copy number of SNP arrays for downstream segmentation, Bioinformatics, 2012 [PMC3381965].
To calibrate (total,fracB) data,
see *calmateByTotalAndFracB()
.
We strongly recommend to always work with (total,fracB) data
instead of (CA,CB) data, because it is much more general.
For further information on the internal fit functions, see
fitCalMaTeInternal
.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 | # Load example (thetaA,thetaB) signals
path <- system.file("exData", package="calmate");
theta <- loadObject("thetaAB,100x2x40.Rbin", path=path);
# Calculate (CA,CB)
thetaR <- matrixStats::rowMedians(theta[,"A",] + theta[,"B",], na.rm=TRUE);
C <- 2*theta/thetaR;
# Calibrate (CA,CB) by CalMaTe
CC <- calmateByThetaAB(theta);
# Plot two "random" arrays
Clim <- c(0,4);
subplots(4, ncol=2, byrow=FALSE);
for (ii in c(1,5)) {
sampleName <- dimnames(C)[[3]][ii];
sampleLabel <- sprintf("Sample #%d ('%s')", ii, sampleName);
plot(C[,,ii], xlim=Clim, ylim=Clim);
title(main=sampleLabel);
plot(CC[,,ii], xlim=Clim, ylim=Clim);
title(main=sprintf("%s\ncalibrated", sampleLabel));
}
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