# Extract, Analyze and Visualize Signatures for Genomic Variations

## Documentation for package ‘sigminer’ version 1.0.7

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

## Help Pages

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
CN.features | Classfication Table of Copy Number Features Devised by Wang et al.
CopyNumber | Class CopyNumber
CopyNumber-class | Class CopyNumber
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_groups | Get Sample Groups from Signature Decomposition Information
get_group_comparison | Get Comparison Result between Signature Groups
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
MAF | Class MAF
MAF-class | Class MAF
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_groups | Show Signature Contribution in Clusters
show_group_comparison | Plot Group Comparison 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 | Show Simplified Signature Number Survey
show_sig_number_survey2 | Show Comprehensive Signature Number Survey
show_sig_profile | Show Signature Profile
sigminer | sigminer: Extract, Analyze and Visualize Signatures for Genomic Variations
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_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
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