copaFilter: Pre-filter Genes for COPA Analysis

In copa: Functions to perform cancer outlier profile analysis.

Description

This function is used to pre-filter genes prior to doing a COPA analysis. The filtering is based on the nth percentile of the outlier samples for each gene. This function is an internal function and not intended to be called by the end user.

Usage

## S4 method for signature 'matrix'
copaFilter(object, cl, cutoff, norm.count, pct)
## S4 method for signature 'data.frame'
copaFilter(object, cl, cutoff, norm.count, pct)
## S4 method for signature 'ExpressionSet'
copaFilter(object, cl, cutoff, norm.count, pct)

Arguments

object	An ExpressionSet, or a matrix or data.frame.
cl	A vector of classlabels indicating sample status (normal = 1, tumor = 2).
cutoff	The cutoff to determine 'outlier' status. See details for more information.
norm.count	The number of normal samples that can be considered 'outliers'. The default is 0, meaning that no normals may be outliers.
pct	The percentile to use for pre-filtering the data. A preliminary step is to compute the number of outlier samples for each gene. All genes with a number of outlier samples less than the (default 95th) percentile will be removed from further consideration.

Value

mat	A matrix containing the gene expression values for the filtered genes.

Author(s)

James W. MacDonald

References

Tomlins, SA, et al. Recurrent fusion of TMPRSS2 and ETS transcription factor genes in prostate cancer. Science. 2005 Oct 28;310(5748):644-8.

copa documentation built on Nov. 8, 2020, 7:47 p.m.