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_maf()

Read MAF Files

read_vcf()

Read VCF files as MAF object

CopyNumber-class

Class CopyNumber

MAF-class

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()

Estimate Signature Number

show_sig_number_survey()

Show Simplified Signature Number Survey

show_sig_number_survey2()

Show Comprehensive Signature Number Survey

sig_extract()

Extract Signatures through NMF

sig_auto_extract()

Extract Signatures through the Automatic Relevance Determination Technique

sigprofiler_extract() sigprofiler_import()

Extract Signatures with SigProfiler

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

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_heatmap()

Show Signature Profile with Heatmap

show_sig_exposure()

Plot Signature Exposure

show_cosmic_sig_profile()

Plot 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

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_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_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

show_group_mapping()

Map Groups using Sankey

enrich_component_strand_bias()

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

Package datasets

Datasets used for signature identification and analysis (some stored in extdata/).

CN.features

Classfication 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.mm10

Location of Centromeres at Genome Build mm10

chromsize.hg19

Chromosome Size of Genome Build hg19

chromsize.hg38

Chromosome Size of Genome Build hg38

chromsize.mm10

Chromosome Size of Genome Build mm10

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

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

Helpers

Helper functions used in the sigminer package.

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_tidy_parameter()

Get Tidy Parameter from Flexmix Model

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

Copy number analysis and visualization

Functions for analyzing copy number data and visualization.

get_cn_ploidy()

Get Ploidy from Absolute 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_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: Extract, Analyze and Visualize Signatures for Genomic Variations