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 |