Extract, Analyze and Visualize Signatures for Genomic Variations


[Up] [Top]

Documentation for package ‘sigminer’ version 1.0.7

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