fitCalMaTe.matrix: Calibrates SNP loci according to the CalMaTe method

In HenrikBengtsson/calmate: Improved Allele-Specific Copy Number of SNP Microarrays for Downstream Segmentation

Calibrates SNP loci according to the CalMaTe method

Description

Calibrates SNP loci according to the CalMaTe method. Note: This is an internal function of the package, which is kept only kept to provide easy access to the internal fit functions. It it actually not elsewhere in the package, and should nor by others.

Usage

## S3 method for class 'matrix'
fitCalMaTe(dataT, references, flavor=c("v2", "v1"), ...)

Arguments

dataT	A 2xI numeric matrix of allele specific copy numbers (ASCNs), where 2 is the number alleles and I is the number of samples.
references	A integer vector with elements in [1,I] specifying which samples should be used as the reference set.
...	Additional arguments passed to the internal fit functions.
flavor	A character string specifying which internal fit function (flavor of the CalMaTe algorithm) to use for fitting the model.

Value

Returns a 2xI numeric matrix of calibrated ASCNs.

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. 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

For further information on the internal fit functions, see fitCalMaTeInternal.

HenrikBengtsson/calmate documentation built on March 21, 2022, 6:32 p.m.