getCNfeatures

This function should not be called directly

Implementation of the classifier described in the paper Ali HR et al (2014) <doi:10.1186/s13059-014-0431-1>. It uses copy number and/or expression form breast cancer data, trains a Tibshirani's 'pamr' classifier with the features available and predicts the iC10 group.

Oscar Rueda

iC10

A Copy Number and Expression-Based Classifier for Breast Tumours

Oscar M Rueda

getCNfeatures function

<dl> <dt>CN</dt>
<dd>CN features matrix</dd> <dt>Probes</dt>
<dd>Vector with the probes to match</dd> <dt>Map</dt>
<dd>data.frame with the genomic description of the features to match</dd> <dt>by.feat</dt>
<dd>"probe" or "gene", indicating if match should be done by probe position or gene name.</dd> <dt>ref</dt>
<dd>hg18 or hg19 (only relevant if matching is done by probe position).</dd> <dt>Synonyms</dt>
<dd>data.frame with available synonym gene names to match (only relevant if matching is done by gene name).</dd></dl>

Arguments

Author

Internal function for matching copy number features. — getCNfeatures

<dl>

 <dt>CN</dt>
<dd>CN features matrix</dd>

 <dt>Probes</dt>
<dd>Vector with the probes to match</dd>

 <dt>Map</dt>
<dd>data.frame with the genomic description of the features to match</dd>

 <dt>by.feat</dt>
<dd>"probe" or "gene", indicating if match should be done by probe position or gene name.</dd>

 <dt>ref</dt>
<dd>hg18 or hg19 (only relevant if matching is done by probe position).</dd>

 <dt>Synonyms</dt>
<dd>data.frame with available synonym gene names to match (only relevant if matching is done by gene name).</dd>

</dl>

getCNfeatures: Internal function for matching copy number features.

Description

Usage

Value

Arguments

Author