To install this package, start R and enter:


In most cases, you don't need to download the package archive at all.


Feature-based association and gene-set enrichment for copy number alteration analysis in cancer

Bioconductor version: 3.0

facopy is an R package for fine-tuned cancer CNA association modeling. Association is measured directly at the genomic features of interest and, in the case of genes, downstream gene-set enrichment analysis can be performed thanks to novel internal processing of the data. The software opens a way to systematically scrutinize the differences in CNA distribution across tumoral phenotypes, such as those that relate to tumor type, location and progression. Currently, the output format from 11 different methods that analyze data from whole-genome/exome sequencing and SNP microarrays, is supported. Multiple genomes, alteration types and variable types are also supported.

Author: David Mosen-Ansorena

Maintainer: David Mosen-Ansorena < at>

Citation (from within R, enter citation("facopy")):


To install this package, start R and enter:



To view documentation for the version of this package installed in your system, start R and enter:



PDF R Script facopy
PDF   Reference Manual
Text   NEWS


biocViews CopyNumberVariation, GeneSetEnrichment, Genetics, GenomicVariation, Microarray, Sequencing, Software, Visualization
Version 1.0.0
In Bioconductor since BioC 3.0 (R-3.1)
License CC BY-NC 4.0
Depends R (>= 3.0), methods, cgdsr (>= 1.1.30), coin (>= 1.0), ggplot2, gridExtra, facopy.annot
Imports annotate, data.table, DOSE, FactoMineR, GO.db, GOstats, graphite, igraph, IRanges, MASS, nnet, reshape2, Rgraphviz, scales
Depends On Me
Imports Me
Suggests Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Package Source facopy_1.0.0.tar.gz
Windows Binary
Mac OS X 10.6 (Snow Leopard) facopy_1.0.0.tgz
Mac OS X 10.9 (Mavericks) facopy_1.0.0.tgz
Browse/checkout source (username/password: readonly)
Package Downloads Report Download Stats

Mailing Lists »

Post questions about Bioconductor packages to our mailing lists. Read the posting guide before posting!

Fred Hutchinson Cancer Research Center