| 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() |
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 |