fitCalMaTeCNprobes.matrix

fitCalMaTeCNprobes

A JxI <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>, where J is the number of loci
 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

Normalizes non-polymorphic copy number loci according to the CalMaTe method.

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

fitCalMaTeCNprobes.matrix function

A JxI <code><a rd-options='base' href='numeric'>numeric</a></code> <code><a rd-options='base' href='matrix'>matrix</a></code>, where J is the number of loci
 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.

fitCalMaTeCNprobes.matrix: Normalizes non-polymorphic copy number loci according to the CalMaTe method

Description

Usage

Arguments

Value