facopy: Feature-based association and gene-set enrichment for copy number alteration analysis in cancer
Version 1.10.0

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.

Browse man pages Browse package API and functions Browse package files

AuthorDavid Mosen-Ansorena
Bioconductor views CopyNumberVariation GeneSetEnrichment Genetics GenomicVariation Microarray Sequencing Software Visualization
Date of publicationNone
MaintainerDavid Mosen-Ansorena <dmosen.gn@cicbiogune.es>
LicenseCC BY-NC 4.0
Version1.10.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("facopy")

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

Functions

addFeatures Man page Source code
addVariables Man page Source code
aggregateInt Source code
allChrs Source code
allCodes Source code
alterCodes Source code
alterationSummary Man page Source code
alterations Source code
calcCallFreqsInt Source code
calcFreqsInt Source code
calculateCor Man page Source code
checkAlter Source code
checkData Source code
checkFeatures Source code
checkFullModel Source code
checkModels Source code
checkSel Source code
checkSelCols Source code
checkVar Source code
checkVarValue Source code
checkYlim Source code
corInt Source code
enrichment Source code
facopy Man page Source code
facopy-package Man page
facopyEnrichment Man page Source code
facopyInfo Man page
facopyInfo-class Man page
facopyPlot Man page Source code
facopyPlotInt Source code
features Source code
fill Source code
genomes Source code
getAlterCodes Source code
getFacopyAnnot Source code
getFacopyInfo Man page Source code
getLOH Source code
getTypeCode Source code
graphPathway Source code
makeArmsInt Source code
makeCor Source code
makeInfo Source code
makeMatrixInt Source code
makeVars Source code
methods Source code
myCalls Man page
myStudy Man page
myVariables Man page
n Source code
ord Source code
pack Source code
plotArm Source code
plotBar Man page Source code
plotBarBps Source code
plotBarFeatures Source code
plotBarInt Source code
plotHist Man page Source code
plotPCA Man page Source code
plotVicinity Source code
plotVicinityInt Source code
plotZoom Man page Source code
preview Man page Source code
printList Source code
readCNData Man page Source code
readFromCNANORM Source code
readFromEXOMECNV Source code
readFromFASTCALL Source code
readFromFREEC Source code
readFromFolder Source code
readFromGAP Source code
readFromInt Source code
readFromONCOSNP Source code
readFromONCOSNPInt Source code
readFromONCOSNPSEQ Source code
readFromPATCHWORK Source code
readFromSEQCNA Source code
readFromTITAN Source code
refcols Source code
sCateg Source code
summary,facopyInfo-method Man page
summary.facopyInfo Source code
types Source code
unLOH Source code
variableCor Man page Source code
variableSummary Man page Source code

Files

DESCRIPTION
NAMESPACE
R
R/AllClasses.R
R/AllGenerics.R
R/facopy_internal_v45.r
R/show-methods.R
R/summary-methods.R
build
build/vignette.rds
data
data/myCalls.rda
data/myStudy.rda
data/myVariables.rda
inst
inst/CITATION
inst/NEWS
inst/doc
inst/doc/facopy.R
inst/doc/facopy.Rnw
inst/doc/facopy.pdf
man
man/addFeatures.Rd
man/addVariables.Rd
man/alterationSummary.Rd
man/calculateCor.Rd
man/facopy-package.Rd
man/facopy.Rd
man/facopyEnrichment.Rd
man/facopyInfo-class.Rd
man/facopyPlot.Rd
man/getFacopyInfo.Rd
man/myCalls.Rd
man/myStudy.Rd
man/myVariables.Rd
man/plotBar.Rd
man/plotHist.Rd
man/plotPCA.Rd
man/plotZoom.Rd
man/preview.Rd
man/readCNData.Rd
man/variableCor.Rd
man/variableSummary.Rd
vignettes
vignettes/enrichmentGO.pdf
vignettes/enrichmentPathway.pdf
vignettes/facopy.Rnw
vignettes/facopy.bib
facopy documentation built on May 20, 2017, 10:41 p.m.