Package: CNVRanger 1.29.1

Introduction | Applicability and Scope | Key functions | Reading and accessing CNV data | Input data format | Representation as a GRangesList | Representation as a RaggedExperiment | Summarizing individual CNV calls across a population | Trimming low-density areas | Reciprocal overlap | Identifying recurrent regions | Overlap analysis of CNVs with functional genomic regions | Finding and illustrating overlaps | Overlap permutation test | CNV-expression association analysis | Application to individual CNV and RNA-seq assays | Application to TCGA data stored in a MultiAssayExperiment | CNV-phenotype association analysis | Setting up a CNV-GWAS | Running a CNV-GWAS | Producing a GDS file in advance | Using relative signal intensities | Session info | References