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

## Documentation for package ‘facopy’ version 1.8.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

facopy-package | facopy: feature-based association and gene-set enrichment for copy number alteration analysis in cancer
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 '"facopyInfo"'
facopyInfo-class | Class '"facopyInfo"'
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
summary-method | Class '"facopyInfo"'
variableCor | Variable Correlations
variableSummary | Variable Summary