CN.features             Classification Table of Copy Number Features
                        Devised by Wang et al. for Method 'W'
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
bp                      A Best Practice for Signature Extraction and
                        Exposure (Activity) Attribution
centromeres.T2T         Location of Centromeres at Genome Build T2T
centromeres.hg19        Location of Centromeres at Genome Build hg19
centromeres.hg38        Location of Centromeres at Genome Build hg38
centromeres.mm10        Location of Centromeres at Genome Build mm10
centromeres.mm9         Location of Centromeres at Genome Build mm9
chromsize.T2T           Chromosome Size of Genome Build T2T
chromsize.hg19          Chromosome Size of Genome Build hg19
chromsize.hg38          Chromosome Size of Genome Build hg38
chromsize.mm10          Chromosome Size of Genome Build mm10
chromsize.mm9           Chromosome Size of Genome Build mm9
cosine                  Calculate Cosine Measures
cytobands.T2T           Location of Chromosome Cytobands at Genome
                        Build T2T
cytobands.hg19          Location of Chromosome Cytobands at Genome
                        Build hg19
cytobands.hg38          Location of Chromosome Cytobands at Genome
                        Build hg38
cytobands.mm10          Location of Chromosome Cytobands at Genome
                        Build mm10
cytobands.mm9           Location of Chromosome Cytobands at Genome
                        Build mm9
enrich_component_strand_bias
                        Performs Strand Bias Enrichment Analysis for a
                        Given Sample-by-Component Matrix
get_Aneuploidy_score    Get Aneuploidy Score from Copy Number Profile
get_adj_p               Get Adjust P Values from Group Comparison
get_bayesian_result     Get Specified Bayesian NMF Result from Run
get_cn_freq_table       Get CNV Frequency Table
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_intersect_size      Get Overlap Size between Interval x and y
get_pLOH_score          Get proportions of pLOH score from Allele
                        Specific Copy Number Profile
get_shannon_diversity_index
                        Get Shannon Diversity Index for Signatures
get_sig_cancer_type_index
                        Obtain Signature Index for Cancer Types
get_sig_db              Get Curated Reference Signature Database
get_sig_exposure        Get Signature Exposure from 'Signature' Object
get_sig_feature_association
                        Calculate Association between Signature
                        Exposures and Other Features
get_sig_rec_similarity
                        Get Reconstructed Profile Cosine Similarity,
                        RSS, etc.
get_sig_similarity      Calculate Similarity between Identified
                        Signatures and Reference Signatures
get_tidy_association    Get Tidy Signature Association Results
group_enrichment        General Group Enrichment Analysis
group_enrichment2       Group Enrichment Analysis with Subsets
handle_hyper_mutation   Handle Hypermutant Samples
hello                   Say Hello to Users
output_bootstrap        Output Signature Bootstrap Fitting Results
output_fit              Output Signature Fitting Results
output_sig              Output Signature Results
output_tally            Output Tally Result in Barplots
read_copynumber         Read Absolute Copy Number Profile
read_copynumber_ascat   Read Copy Number Data from ASCAT Result Files
read_copynumber_seqz    Read Absolute Copy Number Profile from Sequenza
                        Result Directory
read_maf                Read MAF Files
read_sv_as_rs           Read Structural Variation Data as RS object
read_vcf                Read VCF Files as MAF Object
read_xena_variants      Read UCSC Xena Variant Format Data as MAF
                        Object
report_bootstrap_p_value
                        Report P Values from bootstrap Results
same_size_clustering    Same Size Clustering
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_freq_circos     Show Copy Number Variation Frequency Profile
                        with Circos
show_cn_group_profile   Show Summary Copy Number Profile for Sample
                        Groups
show_cn_profile         Show Sample Copy Number Profile
show_cor                A Simple and General Way for Association
                        Analysis
show_cosmic             Show Signature Information in Web Browser
show_cosmic_sig_profile
                        Plot Reference (Mainly COSMIC) Signature
                        Profile
show_group_comparison   Plot Group Comparison Result
show_group_distribution
                        Show Groupped Variable Distribution
show_group_enrichment   Show Group Enrichment 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_profile        Show Signature Profile
show_sig_profile_heatmap
                        Show Signature Profile with Heatmap
show_sig_profile_loop   Show Signature Profile with Loop Way
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_operation           Obtain or Modify Signature Information
sig_tally               Tally a Genomic Alteration Object
sig_unify_extract       An Unified Interface to Extract Signatures
sigprofiler             Extract Signatures with SigProfiler
simulated_catalogs      A List of Simulated SBS-96 Catalog Matrix
simulation              Simulation Analysis
subset.CopyNumber       Subsetting CopyNumber object
transcript.T2T          Merged Transcript Location at Genome Build T2T
transcript.hg19         Merged Transcript Location at Genome Build hg19
transcript.hg38         Merged Transcript Location at Genome Build hg38
transcript.mm10         Merged Transcript Location at Genome Build mm10
transcript.mm9          Merged Transcript Location at Genome Build mm9
transform_seg_table     Transform Copy Number Table
use_color_style         Set Color Style for Plotting
