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
facopy-package          facopy: feature-based association and gene-set
                        enrichment for copy number alteration analysis
                        in cancer
facopyEnrichment        Gene-set Enrichment Analysis
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
variableCor             Variable Correlations
variableSummary         Variable Summary
