calmate (version 0.13.0)

calmateByThetaAB.array: Normalize allele-specific copy numbers (CA,CB)

Description

Normalize allele-specific copy numbers (CA,CB).

Usage

# S3 method for array
calmateByThetaAB(data, references=NULL, ..., truncate=FALSE, refAvgFcn=NULL,
  flavor=c("v2", "v1"), verbose=FALSE)

Arguments

data

An Jx2xI numeric array, where J is the number of SNPs, 2 is the number of alleles, and I is the number of samples.

references

An index vector in [1,I] or a logical vector of length I specifying which samples are used when calculating the reference signals. If NULL, all samples are used. At least 3 samples.

...

Additional arguments passed to the internal fit function fitCalMaTeInternal.

truncate

If TRUE, final ASCNs are forced to be non-negative while preserving the total CNs.

refAvgFcn

(optional) A function that takes a JxI numeric matrix an argument na.rm and returns a numeric vector of length J. It should calculate some type of average for each of the J rows, e.g. rowMedians. If specified, then the total copy numbers of the calibrated ASCNs are standardized toward (twice) the average of the total copy numbers of the calibrated reference ASCNs.

flavor

A character string specifying which flavor of the CalMaTe algorithm to use for fitting the model.

verbose

See Verbose.

Value

Returns an Jx2xI numeric array with the same dimension names as argument data.

Flavors

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.

References

[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].

See Also

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.

Examples

# NOT RUN {
# 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));
}
# }