CN.features             Classfication Table of Copy Number Features
                        Devised by Wang et al.
CopyNumber-class        Class CopyNumber
MAF-class               Class MAF
add_h_arrow             Add Horizontal Arrow with Text Label to a
                        ggplot
add_labels              Add Text Labels to a ggplot
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
cytobands.hg19          Location of Chromosome Cytobands at Genome
                        Build hg19
cytobands.hg38          Location of Chromosome Cytobands at Genome
                        Build hg38
enrich_component_strand_bias
                        Performs Strand Bias Enrichment Analysis for a
                        Given Sample-by-Component Matrix
get_adj_p               Get Adjust P Values from Group Comparison
get_bayesian_result     Get Specified Bayesian NMF Result from Run
get_cn_ploidy           Get Ploidy from Absolute Copy Number Profile
get_genome_annotation   Get Genome Annotation
get_group_comparison    Get Comparison Result between Signature Groups
get_groups              Get Sample Groups from Signature Decomposition
                        Information
get_sig_exposure        Get Signature Exposure from 'Signature' Object
get_sig_feature_association
                        Calculate Association between Signature
                        Exposures and Other Features
get_sig_similarity      Calculate Similarity between Identified
                        Signatures and Reference Signatures
get_tidy_association    Get Tidy Signature Association Results
get_tidy_parameter      Get Tidy Parameter from Flexmix Model
handle_hyper_mutation   Handle Hypermutant Samples
hello                   Say Hello to Users
read_copynumber         Read Absolute Copy Number Profile
read_maf                Read MAF Files
report_bootstrap_p_value
                        Report P Values from bootstrap Results
scoring                 Score Copy Number Profile
show_catalogue          Show Alteration Catalogue Profile
show_cn_circos          Show Copy Number Profile in Circos
show_cn_components      Show Copy Number Components
show_cn_distribution    Show Copy Number Distribution either by Length
                        or Chromosome
show_cn_features        Show Copy Number Feature Distributions
show_cn_profile         Show Sample Copy Number Profile
show_cosmic_sig_profile
                        Plot COSMIC Signature Profile
show_group_comparison   Plot Group Comparison Result
show_group_mapping      Map Groups using Sankey
show_groups             Show Signature Contribution in Clusters
show_sig_bootstrap      Show Signature Bootstrap Analysis Results
show_sig_consensusmap   Show Signature Consensus Map
show_sig_exposure       Plot Signature Exposure
show_sig_feature_corrplot
                        Draw Corrplot for Signature Exposures and Other
                        Features
show_sig_fit            Show Signature Fit Result
show_sig_number_survey
                        Show Simplified Signature Number Survey
show_sig_number_survey2
                        Show Comprehensive Signature Number Survey
show_sig_profile        Show Signature Profile
sig_auto_extract        Extract Signatures through the Automatic
                        Relevance Determination Technique
sig_convert             Convert Signatures between different Genomic
                        Distribution of Components
sig_estimate            Estimate Signature Number
sig_extract             Extract Signatures through NMF
sig_fit                 Fit Signature Exposures with Linear Combination
                        Decomposition
sig_fit_bootstrap       Obtain Bootstrap Distribution of Signature
                        Exposures of a Certain Tumor Sample
sig_fit_bootstrap_batch
                        Exposure Instability Analysis of Signature
                        Exposures with Bootstrapping
sig_names               Obtain or Modify Signature Information
sig_tally               Tally a Genomic Alteration Object
sigminer                sigminer: Extract, Analyze and Visualize
                        Signatures for Genomic Variations
subset.CopyNumber       Subsetting CopyNumber object
transcript.hg19         Merged Transcript Location at Genome Build hg19
transcript.hg38         Merged Transcript Location at Genome Build hg38
use_color_style         Set Color Style for Plotting
