CopyNumber-class        Class CopyNumber
GenomicVariation-class
                        Class GenomicVariation
MAF-class               Class MAF
centromeres.hg19        location of centromeres at genome build hg19
centromeres.hg38        location of centromeres at genome build hg38
chromsize.hg19          chromosome size of genome build hg19
chromsize.hg38          chromosome size of genome build hg38
draw_cn_components      Plot mixture fit model components
draw_cn_distribution    Plot copy number distribution either by length
                        or chromosome
draw_cn_features        Plot copy number feature distribution
draw_sig_activity       Plot signature activity
draw_sig_corrplot       Plot correlation between signature activities
draw_sig_profile        Plot signature profile
draw_subtypes_comparison
                        Plot comparison between signature subtypes
get_ArmLocation         Get chromosome arm location
get_LengthFraction      Calculate length fraction profile of copy
                        number
get_cnlist              Extract copy number profile as list from
                        CopyNumber object
get_cnsummary_sample    Get summary of copy number variation per sample
get_components          Fit optimal number of mixture model components
get_features            Derive copy number feature distributions
get_matrix              Generate a sample-by-component matrix
hello                   Say hello to users
prepare_copynumber      Prepare nmf input matrix for copy number
                        signature analysis
prepare_maf             Prepare nmf input matrix for mutational
                        signature analysis
read_copynumber         Read absolute copy number profile
read_maf                Read MAF files.
read_variation          Read genomic variation profile
sig_assign_samples      Return sample clustering from NMF run results
sig_estimate            Estimate signature number
sig_extract             Extract variation signatures
sig_get_activity        Get signature activity
sig_get_correlation     Get correlation matrix between signature
                        activities
sig_get_similarity      Get similarity between signatures
sig_prepare             Prepare variation signature analysis
sig_summarize_subtypes
                        Get summary of signature subtypes
sigminer                sigminer: Capture Genomic Variation Signatures
                        using Non-Negative Matrix Factorization
subset.CopyNumber       Subsetting CopyNumber object
test_run_components     Test running status for getting components
