# Extract, Analyze and Visualize Mutational Signatures for Genomic Variations

## Documentation for package ‘sigminer’ version 2.3.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

A B C E G H M O R S T U

## -- A --

add_h_arrow | Add Horizontal Arrow with Text Label to a ggplot
add_labels | Add Text Labels to a ggplot

## -- B --

bp | A Best Practice for Signature Extraction and Exposure (Activity) Attribution
bp_attribute_activity | A Best Practice for Signature Extraction and Exposure (Activity) Attribution
bp_cluster_iter_list | A Best Practice for Signature Extraction and Exposure (Activity) Attribution
bp_extract_signatures | A Best Practice for Signature Extraction and Exposure (Activity) Attribution
bp_extract_signatures_iter | A Best Practice for Signature Extraction and Exposure (Activity) Attribution
bp_get_clustered_sigs | A Best Practice for Signature Extraction and Exposure (Activity) Attribution
bp_get_rank_score | A Best Practice for Signature Extraction and Exposure (Activity) Attribution
bp_get_sig_obj | A Best Practice for Signature Extraction and Exposure (Activity) Attribution
bp_get_stats | A Best Practice for Signature Extraction and Exposure (Activity) Attribution
bp_show_survey | A Best Practice for Signature Extraction and Exposure (Activity) Attribution
bp_show_survey2 | A Best Practice for Signature Extraction and Exposure (Activity) Attribution

## -- C --

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
centromeres.T2T | Location of Centromeres at 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
chromsize.T2T | Chromosome Size of Genome Build T2T
CN.features | Classification Table of Copy Number Features Devised by Wang et al. for Method 'W'
CopyNumber | Class CopyNumber
CopyNumber-class | Class CopyNumber
cosine | Calculate Cosine Measures
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
cytobands.T2T | Location of Chromosome Cytobands at Genome Build T2T

## -- E --

enrich_component_strand_bias | Performs Strand Bias Enrichment Analysis for a Given Sample-by-Component Matrix

## -- G --

get_adj_p | Get Adjust P Values from Group Comparison
get_Aneuploidy_score | Get Aneuploidy Score from Copy Number Profile
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_groups | Get Sample Groups from Signature Decomposition Information
get_group_comparison | Get Comparison Result between Signature Groups
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

## -- H --

handle_hyper_mutation | Handle Hypermutant Samples
hello | Say Hello to Users

## -- M --

MAF | Class MAF
MAF-class | Class MAF

## -- O --

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

## -- R --

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_maf_minimal | 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

## -- S --

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_groups | Show Signature Contribution in Clusters
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_sig_bootstrap | Show Signature Bootstrap Analysis Results
show_sig_bootstrap_error | Show Signature Bootstrap Analysis Results
show_sig_bootstrap_exposure | Show Signature Bootstrap Analysis Results
show_sig_bootstrap_stability | 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 | Estimate Signature Number
show_sig_number_survey2 | Estimate Signature Number
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
sigprofiler | Extract Signatures with SigProfiler
sigprofiler_extract | Extract Signatures with SigProfiler
sigprofiler_import | Extract Signatures with SigProfiler
sigprofiler_reorder | Extract Signatures with SigProfiler
sig_attrs | Obtain or Modify Signature Information
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_exposure | Obtain or Modify Signature Information
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_modify_names | Obtain or Modify Signature Information
sig_names | Obtain or Modify Signature Information
sig_number | Obtain or Modify Signature Information
sig_operation | Obtain or Modify Signature Information
sig_signature | Obtain or Modify Signature Information
sig_tally | Tally a Genomic Alteration Object
sig_tally.CopyNumber | Tally a Genomic Alteration Object
sig_tally.MAF | Tally a Genomic Alteration Object
sig_tally.RS | Tally a Genomic Alteration Object
sig_unify_extract | An Unified Interface to Extract Signatures
simulated_catalogs | A List of Simulated SBS-96 Catalog Matrix
simulate_catalogue | Simulation Analysis
simulate_catalogue_matrix | Simulation Analysis
simulate_signature | Simulation Analysis
simulation | Simulation Analysis
subset.CopyNumber | Subsetting CopyNumber object

## -- T --

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
transcript.T2T | Merged Transcript Location at Genome Build T2T
transform_seg_table | Transform Copy Number Table

## -- U --

use_color_style | Set Color Style for Plotting