copa: Functions to perform cancer outlier profile analysis.
Version 1.44.0

COPA is a method to find genes that undergo recurrent fusion in a given cancer type by finding pairs of genes that have mutually exclusive outlier profiles.

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AuthorJames W. MacDonald
Bioconductor views DifferentialExpression OneChannel TwoChannel Visualization
Date of publicationNone
MaintainerJames W. MacDonald <jmacdon@u.washington.edu>
LicenseArtistic-2.0
Version1.44.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("copa")

Man pages

copa: Calculate COPA Scores from a Set of Microarrays
copaFilter: Pre-filter Genes for COPA Analysis
copa.package: copa - A package to compute 'Cancer Outlier Profile Analysis'
copaPerm: Measure Significance of COPA by Permutation
copaTable: Summarize copa results
getans: Interactive Function
perm.mat: Produce a Matrix of Permuted Classlabels
plotCopa: Plot Gene Pairs fom the Results of Running copa
pSum: Compute all pairwise sums
scatterPlotCopa: Create scatterplots of interesting gene pairs
summaryCopa: Create Summary Showing Top Gene Pairs

Functions

copa Man page Source code
copa-package Man page
copaFilter Man page
copaFilter, ExpressionSet-method Man page
copaFilter, data.frame-method Man page
copaFilter, matrix-method Man page
copaFilter-methods Man page
copaPerm Man page Source code
do.copaFilter Man page Source code
getans Man page Source code
onUnload Source code
pSum Man page Source code
perm.mat Man page Source code
plotCopa Man page Source code
scatterPlotCopa Man page Source code
summaryCopa Man page Source code
tableCopa Man page Source code

Files

DESCRIPTION
NAMESPACE
R
R/AllMethods.R
R/copa.R
R/zzz.R
build
build/vignette.rds
inst
inst/CITATION
inst/doc
inst/doc/copa.R
inst/doc/copa.Rnw
inst/doc/copa.pdf
man
man/copa.Rd
man/copa.package.Rd
man/copaFilter.Rd
man/copaPerm.Rd
man/copaTable.Rd
man/getans.Rd
man/pSum.Rd
man/perm.mat.Rd
man/plotCopa.Rd
man/scatterPlotCopa.Rd
man/summaryCopa.Rd
src
src/copa.c
vignettes
vignettes/copa.Rnw
vignettes/copa.bib
copa documentation built on May 20, 2017, 9:21 p.m.