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


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Documentation for package ‘facopy’ version 1.3.1

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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