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

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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
Date of publication
None
Maintainer
David Mosen-Ansorena <dmosen.gn@cicbiogune.es>
License
CC BY-NC 4.0
Version
1.8.0

View on Bioconductor

Man pages

addFeatures
Add Feature Annotation
addVariables
Add Variable Annotation
alterationSummary
Alteration Summary
calculateCor
Calculate Correlation Between Copy Number and Expression
facopy
Feature-Based Copy Number Association Analysis
facopyEnrichment
Gene-set Enrichment Analysis
facopyInfo-class
Class '"facopyInfo"'
facopy-package
facopy: feature-based association and gene-set enrichment for...
facopyPlot
Plot a Genome-Wide Overview of Association Results
getFacopyInfo
List Available facopy Input and Characteristics
myCalls
Example facopy Object with Just Copy Number Calls
myStudy
Example Complete facopy Object
myVariables
Example Phenotypic Annotation
plotBar
Overview of Alterations by Chromosome Arm
plotHist
Stacked Histograms
plotPCA
facopy PCA
plotZoom
Zoom In to Plot a Chromosome Arm or a Genomic Feature
preview
Alteration and Varible Preview
readCNData
Read Copy Number Data
variableCor
Variable Correlations
variableSummary
Variable Summary

Files in this package

facopy/DESCRIPTION
facopy/NAMESPACE
facopy/R
facopy/R/AllClasses.R
facopy/R/AllGenerics.R
facopy/R/facopy_internal_v45.r
facopy/R/show-methods.R
facopy/R/summary-methods.R
facopy/build
facopy/build/vignette.rds
facopy/data
facopy/data/myCalls.rda
facopy/data/myStudy.rda
facopy/data/myVariables.rda
facopy/inst
facopy/inst/CITATION
facopy/inst/NEWS
facopy/inst/doc
facopy/inst/doc/facopy.R
facopy/inst/doc/facopy.Rnw
facopy/inst/doc/facopy.pdf
facopy/man
facopy/man/addFeatures.Rd
facopy/man/addVariables.Rd
facopy/man/alterationSummary.Rd
facopy/man/calculateCor.Rd
facopy/man/facopy-package.Rd
facopy/man/facopy.Rd
facopy/man/facopyEnrichment.Rd
facopy/man/facopyInfo-class.Rd
facopy/man/facopyPlot.Rd
facopy/man/getFacopyInfo.Rd
facopy/man/myCalls.Rd
facopy/man/myStudy.Rd
facopy/man/myVariables.Rd
facopy/man/plotBar.Rd
facopy/man/plotHist.Rd
facopy/man/plotPCA.Rd
facopy/man/plotZoom.Rd
facopy/man/preview.Rd
facopy/man/readCNData.Rd
facopy/man/variableCor.Rd
facopy/man/variableSummary.Rd
facopy/vignettes
facopy/vignettes/enrichmentGO.pdf
facopy/vignettes/enrichmentPathway.pdf
facopy/vignettes/facopy.Rnw
facopy/vignettes/facopy.bib