Extract, Analyze and Visualize Mutational Signatures for Genomic
Variations
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Documentation for package ‘sigminer’ version 2.3.1
Help Pages
-- 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 |