fitCalMaTe.matrix

fitCalMaTe

A 2xI <code><a rd-options="base" href="/link/numeric?package=calmate&version=0.13.0&to=base" data-mini-rdoc="base::numeric">numeric</a></code> <code><a rd-options="base" href="/link/matrix?package=calmate&version=0.13.0&to=base" data-mini-rdoc="base::matrix">matrix</a></code> of allele specific copy numbers (ASCNs),
 where 2 is the number alleles and I is the number of samples.

dataT

A <code><a rd-options="base" href="/link/integer?package=calmate&version=0.13.0&to=base" data-mini-rdoc="base::integer">integer</a></code> <code><a rd-options="base" href="/link/vector?package=calmate&version=0.13.0&to=base" data-mini-rdoc="base::vector">vector</a></code> with elements in [1,I] specifying
 which samples should be used as the reference set.

references

Additional arguments passed to the internal fit functions.

A <code><a rd-options="base" href="/link/character?package=calmate&version=0.13.0&to=base" data-mini-rdoc="base::character">character</a></code> string specifying which internal fit function
 (flavor of the CalMaTe algorithm) to use for fitting the model.

flavor

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.

methods

internal

The CalMaTe method calibrates preprocessed allele-specific copy number estimates (ASCNs) from DNA microarrays by controlling for single-nucleotide polymorphism-specific allelic crosstalk. The resulting ASCNs are on average more accurate, which increases the power of segmentation methods for detecting changes between copy number states in tumor studies including copy neutral loss of heterozygosity. CalMaTe applies to any ASCNs regardless of preprocessing method and microarray technology, e.g. Affymetrix and Illumina.

Henrik Bengtsson

calmate

Improved Allele-Specific Copy Number of SNP Microarrays for
Downstream Segmentation

Maria Ortiz

Ander Aramburu

Pierre Neuvial

Angel Rubio

fitCalMaTe.matrix function

For backward compatibility, we try to keep all major versions of
 the CalMaTe algorithm available. Older versions can be used by
 specifying argument <code>flavor</code>.
 For more information about the different flavors,
 see <code><a rd-options="" href="/link/fitCalMaTeInternal?package=calmate&version=0.13.0" data-mini-rdoc="calmate::fitCalMaTeInternal">fitCalMaTeInternal</a></code>.

Flavors

A 2xI <code><a rd-options='base' href='numeric'>numeric</a></code> <code><a rd-options='base' href='matrix'>matrix</a></code> of allele specific copy numbers (ASCNs),
 where 2 is the number alleles and I is the number of samples.

A <code><a rd-options='base' href='integer'>integer</a></code> <code><a rd-options='base' href='vector'>vector</a></code> with elements in [1,I] specifying
 which samples should be used as the reference set.

A <code><a rd-options='base' href='character'>character</a></code> string specifying which internal fit function
 (flavor of the CalMaTe algorithm) to use for fitting the model.

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

For backward compatibility, we try to keep all major versions of
 the CalMaTe algorithm available. Older versions can be used by
 specifying argument <code>flavor</code>.
 For more information about the different flavors,
 see <code><a rd-options='' href='fitCalMaTeInternal'>fitCalMaTeInternal</a></code>.

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

Description

Usage

Arguments

Value

Flavors

References

See Also