copa: Functions to perform cancer outlier profile analysis.

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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.

Author
James W. MacDonald
Date of publication
None
Maintainer
James W. MacDonald <jmacdon@u.washington.edu>
License
Artistic-2.0
Version
1.42.0

View on Bioconductor

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

Files in this package

copa/DESCRIPTION
copa/NAMESPACE
copa/R
copa/R/AllMethods.R
copa/R/copa.R
copa/R/zzz.R
copa/build
copa/build/vignette.rds
copa/inst
copa/inst/CITATION
copa/inst/doc
copa/inst/doc/copa.R
copa/inst/doc/copa.Rnw
copa/inst/doc/copa.pdf
copa/man
copa/man/copa.Rd
copa/man/copa.package.Rd
copa/man/copaFilter.Rd
copa/man/copaPerm.Rd
copa/man/copaTable.Rd
copa/man/getans.Rd
copa/man/pSum.Rd
copa/man/perm.mat.Rd
copa/man/plotCopa.Rd
copa/man/scatterPlotCopa.Rd
copa/man/summaryCopa.Rd
copa/src
copa/src/copa.c
copa/vignettes
copa/vignettes/copa.Rnw
copa/vignettes/copa.bib