Package index • sigminer

Data input, classes and operation Read genomic variation data as an R object and more.
`read_copynumber()`	Read Absolute Copy Number Profile
`read_copynumber_seqz()`	Read Absolute Copy Number Profile from Sequenza Result Directory
`read_copynumber_ascat()`	Read Copy Number Data from ASCAT Result Files
`read_maf()` `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
`CopyNumber-class` `CopyNumber`	Class CopyNumber
`MAF-class` `MAF`	Class MAF
`subset(<CopyNumber>)`	Subsetting CopyNumber object
Core pipeline 1 - de novo signature identification Identify signatures from genomic variation profile. After reading data, the following functions construct the standard pipeline for most users.
`sig_tally()`	Tally a Genomic Alteration Object
`handle_hyper_mutation()`	Handle Hypermutant Samples
`sig_estimate()` `show_sig_number_survey()` `show_sig_number_survey2()`	Estimate Signature Number
`sig_unify_extract()`	An Unified Interface to Extract Signatures
`sig_extract()`	Extract Signatures through NMF
`sig_auto_extract()`	Extract Signatures through the Automatic Relevance Determination Technique
`sigprofiler_extract()` `sigprofiler_import()` `sigprofiler_reorder()`	Extract Signatures with SigProfiler
`bp_extract_signatures()` `bp_extract_signatures_iter()` `bp_cluster_iter_list()` `bp_get_clustered_sigs()` `bp_get_sig_obj()` `bp_get_stats()` `bp_get_rank_score()` `bp_show_survey2()` `bp_show_survey()` `bp_attribute_activity()`	A Best Practice for Signature Extraction and Exposure (Activity) Attribution
Core pipeline 2 - signature exposure fitting and optimization Quantify exposure in at least one sample with reference signatures. It can also be used to optimize signature exposure from pipeline 1 and analyze exposure instability.
`sig_tally()`	Tally a Genomic Alteration Object
`handle_hyper_mutation()`	Handle Hypermutant Samples
`get_sig_cancer_type_index()`	Obtain Signature Index for Cancer Types
`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
`report_bootstrap_p_value()`	Report P Values from bootstrap Results
Signature visualization Show signature profile and exposure.
`show_catalogue()`	Show Alteration Catalogue Profile
`show_sig_profile()`	Show Signature Profile
`show_sig_profile_loop()`	Show Signature Profile with Loop Way
`show_sig_profile_heatmap()`	Show Signature Profile with Heatmap
`show_sig_exposure()`	Plot Signature Exposure
`show_cosmic()`	Show Signature Information in Web Browser
`show_cosmic_sig_profile()`	Plot Reference (Mainly COSMIC) Signature Profile
`show_sig_consensusmap()`	Show Signature Consensus Map
Fit and bootstrap visualization Show signature fit and bootstrap analysis results.
`show_sig_fit()`	Show Signature Fit Result
`show_sig_bootstrap_exposure()` `show_sig_bootstrap_error()` `show_sig_bootstrap_stability()`	Show Signature Bootstrap Analysis Results
Output analysis results to local machine Save results and plots as files. For automatic analysis, please use sigflow.
`output_tally()`	Output Tally Result in Barplots
`output_sig()`	Output Signature Results
`output_fit()`	Output Signature Fitting Results
`output_bootstrap()`	Output Signature Bootstrap Fitting Results
Signature object operation Obtain or modify `Signature` object information.
`sig_names()` `sig_modify_names()` `sig_number()` `sig_attrs()` `sig_signature()` `sig_exposure()`	Obtain or Modify Signature Information
Signature analysis and corresponding visualization Analyze signatures and output the result to visualization.
`get_sig_similarity()`	Calculate Similarity between Identified Signatures and Reference Signatures
`get_sig_rec_similarity()`	Get Reconstructed Profile Cosine Similarity, RSS, etc.
`get_sig_exposure()`	Get Signature Exposure from 'Signature' Object
`get_sig_feature_association()`	Calculate Association between Signature Exposures and Other Features
`get_tidy_association()`	Get Tidy Signature Association Results
`show_cor()`	A Simple and General Way for Association Analysis
`show_sig_feature_corrplot()`	Draw Corrplot for Signature Exposures and Other Features
`show_groups()`	Show Signature Contribution in Clusters
`get_groups()`	Get Sample Groups from Signature Decomposition Information
`get_group_comparison()`	Get Comparison Result between Signature Groups
`show_group_comparison()`	Plot Group Comparison Result
`group_enrichment()`	General Group Enrichment Analysis
`show_group_enrichment()`	Show Group Enrichment Result
`group_enrichment2()`	Group Enrichment Analysis with Subsets
`show_group_distribution()`	Show Groupped Variable Distribution
`show_group_mapping()`	Map Groups using Sankey
`enrich_component_strand_bias()`	Performs Strand Bias Enrichment Analysis for a Given Sample-by-Component Matrix
`simulate_signature()` `simulate_catalogue()` `simulate_catalogue_matrix()`	Simulation Analysis
`get_shannon_diversity_index()`	Get Shannon Diversity Index for Signatures
Package datasets Datasets used for signature identification and analysis (some stored in `extdata/`).
`simulated_catalogs`	A List of Simulated SBS-96 Catalog Matrix
`CN.features`	Classification Table of Copy Number Features Devised by Wang et al. for Method 'W'
`centromeres.hg19`	Location of Centromeres at Genome Build hg19
`centromeres.hg38`	Location of Centromeres at Genome Build hg38
`centromeres.T2T`	Location of Centromeres at Genome Build T2T
`centromeres.mm10`	Location of Centromeres at Genome Build mm10
`centromeres.mm9`	Location of Centromeres at Genome Build mm9
`chromsize.hg19`	Chromosome Size of Genome Build hg19
`chromsize.hg38`	Chromosome Size of Genome Build hg38
`chromsize.T2T`	Chromosome Size of Genome Build T2T
`chromsize.mm10`	Chromosome Size of Genome Build mm10
`chromsize.mm9`	Chromosome Size of Genome Build mm9
`cytobands.hg19`	Location of Chromosome Cytobands at Genome Build hg19
`cytobands.hg38`	Location of Chromosome Cytobands at Genome Build hg38
`cytobands.T2T`	Location of Chromosome Cytobands at Genome Build T2T
`cytobands.mm10`	Location of Chromosome Cytobands at Genome Build mm10
`cytobands.mm9`	Location of Chromosome Cytobands at Genome Build mm9
`transcript.hg19`	Merged Transcript Location at Genome Build hg19
`transcript.hg38`	Merged Transcript Location at Genome Build hg38
`transcript.T2T`	Merged Transcript Location at Genome Build T2T
`transcript.mm10`	Merged Transcript Location at Genome Build mm10
`transcript.mm9`	Merged Transcript Location at Genome Build mm9
Helpers Helper functions used in the sigminer package.
`get_sig_db()`	Get Curated Reference Signature Database
`sig_convert()`	Convert Signatures between different Genomic Distribution of Components
`get_genome_annotation()`	Get Genome Annotation
`get_bayesian_result()`	Get Specified Bayesian NMF Result from Run
`get_adj_p()`	Get Adjust P Values from Group Comparison
`use_color_style()`	Set Color Style for Plotting
`add_h_arrow()`	Add Horizontal Arrow with Text Label to a ggplot
`add_labels()`	Add Text Labels to a ggplot
`cosine()`	Calculate Cosine Measures
`get_cn_freq_table()`	Get CNV Frequency Table
`same_size_clustering()`	Same Size Clustering
`get_intersect_size()`	Get Overlap Size between Interval x and y
Copy number analysis and visualization Functions for analyzing copy number data and visualization.
`transform_seg_table()`	Transform Copy Number Table
`get_cn_ploidy()`	Get Ploidy from Absolute Copy Number Profile
`get_Aneuploidy_score()`	Get Aneuploidy Score from Copy Number Profile
`get_pLOH_score()`	Get proportions of pLOH score from Allele Specific Copy Number Profile
`scoring()`	Score Copy Number Profile
`show_cn_profile()`	Show Sample Copy Number Profile
`show_cn_circos()`	Show Copy Number Profile in Circos
`show_cn_group_profile()`	Show Summary Copy Number Profile for Sample Groups
`show_cn_freq_circos()`	Show Copy Number Variation Frequency Profile with Circos
`show_cn_distribution()`	Show Copy Number Distribution either by Length or Chromosome
`show_cn_features()`	Show Copy Number Feature Distributions
`show_cn_components()`	Show Copy Number Components
Extra documentation Extra function and introduction.
`hello()`	Say Hello to Users
`sigminer` `sigminer-package`	sigminer: Extract, Analyze and Visualize Signatures for Genomic Variations

Reference

Data input, classes and operation

Core pipeline 1 - de novo signature identification

Core pipeline 2 - signature exposure fitting and optimization

Signature visualization

Fit and bootstrap visualization

Output analysis results to local machine

Signature object operation

Signature analysis and corresponding visualization

Package datasets

Helpers

Copy number analysis and visualization

Extra documentation