pam50centroids

The dataset corresponds to the Permutation-Based Confidence for Molecular
Classification package <code><a rd-options="" href="/link/PAM50?package=pbcmc&version=1.0.0" data-mini-rdoc="pbcmc::PAM50">PAM50</a></code> example objects, that was 
<code><a rd-options="" href="/link/filtrate?package=pbcmc&version=1.0.0" data-mini-rdoc="pbcmc::filtrate">filtrate</a></code>d, <code><a rd-options="" href="/link/classify?package=pbcmc&version=1.0.0" data-mini-rdoc="pbcmc::classify">classify</a></code>ed and 
<code><a rd-options="" href="/link/permutate?package=pbcmc&version=1.0.0" data-mini-rdoc="pbcmc::permutate">permutate</a></code>d using the following parameters:
<dl>
 <dt>Permutations</dt><dd>10000</dd> <dt>fdr</dt><dd>0.01</dd> <dt>corCutoff</dt><dd>0.1</dd> <dt>keep</dt><dd>TRUE</dd></dl>

datasets

centroids

pam50

The pbcmc package characterizes uncertainty assessment on
gene expression classifiers, a. k. a. molecular signatures,
based on a permutation test. In order to achieve this goal,
synthetic simulated subjects are obtained by permutations of
gene labels. Then, each synthetic subject is tested against the
corresponding subtype classifier to build the null
distribution. Thus, classification confidence measurement can
be provided for each subject, to assist physician therapy
choice. At present, it is only available for PAM50
implementation in genefu package but it can easily be extend to
other molecular signatures.

Cristobal Fresno

pbcmc

Permutation-Based Confidence for Molecular Classification

pam50centroids function

pam50centroids corresponds with pam50$centroids dataset 
available in genefu package.

Format

The dataset corresponds to the Permutation-Based Confidence for Molecular
Classification package <code><a href="PAM50" rd-options="">PAM50</a></code> example objects, that was 
<code><a href="filtrate" rd-options="">filtrate</a></code>d, <code><a href="classify" rd-options="">classify</a></code>ed and 
<code><a href="permutate" rd-options="">permutate</a></code>d using the following parameters:
[object Object],[object Object],[object Object],[object Object]

pam50centroids: Example PAM50 objects for pbcmc package

Description

Usage

Arguments

Value

Format

References

See Also