Quantify and visualize variability of mutational signatures within and across samples

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Documentation for package ‘sigvar’ version 0.99.8

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all_sig_pal Color palette for mutational signatures analyzed in the study by Morrison et al.
carcinogens_mice_SBS Single base substitution signature attributions found in mice exposed to 20 known or suspected carcinogens.
carcinogens_mice_SBS.refs Reference single base substitution signatures found in mice exposed to 20 known or suspected carcinogens.
COSMIC3.0_ID Indel reference signatures for COSMIC3.0
COSMIC3.0_SBS Single base substitution reference signatures for COSMIC3.0
COSMIC3.1_CN Copy Number reference signatures for COSMIC3.1
COSMIC3.3.1_SBS Single base substitution reference signatures for COSMIC3.3.1
COSMIC3.3.1_SBS_mm10 Mice Single base substitution reference signatures for COSMIC3.3.1
COSMIC3.3_CN Copy Number reference signatures for COSMIC3.3
COSMIC3.3_DBS Double base reference signatures for COSMIC3.0
COSMIC3.3_DBS_mm10 Mice Double base reference signatures for COSMIC3.0
COSMIC3.3_ID Indel reference signatures for COSMIC3.3.1
cossim Compute the cosine similarity matrix for a set of mutational signatures.
EGFR_context_counts_ordered Counts of each context class for the main transcript of gene EGFR
EGFR_drivers_intogen_SBS96 SBS96 spectrum from the intogen website for gene EGFR in lung adenocarcinomas
ESCC_countries_SBS Single base substitution signature attributions found in esophageal squamous cell carcinoma across countries with varying incidence.
ESCC_countries_SBS.refs Reference COSMIC Single base substitution signatures found in esophageal squamous cell carcinoma across countries with varying incidence.
ESCC_sig_activity Activity of SBS, DBS, and ID mutational signatures in a global sample of esophageal squamous cell carcinoma cases.
ESCC_sig_similarity Cosine similarity of SBS, DBS, and ID mutational signatures found in a global sample of esophageal squamous cell carcinoma cases.
fst Compute the Fst of a matrix of compositional vectors
fst_norm Compute the normalized Fst of a matrix of compositional vectors
get_SBS96_driver_spectrum get_SBS96_driver_spectrum
get_SBS96_spectrum get_SBS96_spectrum
het Compute the Gini-Simpson index of a compositional vector
het_mean Compute the mean Gini-Simpson index of the rows in a matrix of compositional vectors
het_pooled Compute the pooled Gini-Simpson index of the rows in a matrix of compositional vectors
import_SigProfiler import_SigProfiler
Intogen_EGFR_LUAD Driver mutations from the intogen website for gene EGFR in lung adenocarcinomas
MESOMICS_CN_SBS Copy Number and Single Base Substitution mutational signatures for 120 malignant pleural mesothelioma from the MESOMICS cohort
mutsig_carcinogens_mice_bootstrap_p_vals Bootstrap p-values comparing SVA results for carcinogen-exposed murine tumors to spontaneous tumors
mutsig_carcinogens_mice_SBS Single Base Substitution mutational signatures for 181 mice exposed to known or suspected carcinogens
mutsig_carcinogens_mice_SBS.refs Definitions of murine single base substitution mutational signatures
PCAWG_SigProfiler_COSMIC_DBS Double Base Substitution COSMIC mutational signatures for 2780 tumors
PCAWG_SigProfiler_COSMIC_ID Indel COSMIC mutational signatures for 2780 tumors
PCAWG_SigProfiler_COSMIC_SBS Single Base Substitution COSMIC mutational signatures for 2780 tumors
plot_dots Plot the mean mutational signature activities of each group of samples
plot_SBS_spectrum Plot an SBS mutational spectrum
plot_signature_prop Visualize a relative abundance matrix as a stacked bar plot.
radiation_sigs_morton Single base substitution signature attributions found in papillary thyroid carcinoma from Chernobyl incident survivors.
radiation_sigs_morton_cossim Cosine similarity matrix of Single base substitution signatures found in papillary thyroid carcinoma from Chernobyl incident survivors.
rcc_sig_activity Activity of SBS, DBS, and ID mutational signatures in a global sample of renal cell carcinoma cases.
rcc_sim Activity of SBS, DBS, and ID mutational signatures in a global sample of renal cell carcinoma cases.
sbs_palette Single Base Substitution COSMIC mutational signatures for 2780 tumors
Sherlock_LCINS.metadata Metadata accompanying mutational signatures for lung cancer in never smokers.
Sherlock_LCINS_SBS Single base substitution signature attributions found in Lung cancer in never smokers.
Sherlock_LCINS_SBS.refs Reference COSMIC Single base substitution signatures found in Lung cancer in never smokers.
sigboot Statistically compare the within-sample diversity and across-sample heterogeneity of the mutational signature activity in two or more groups of tumor samples.
sigvar Compute the within-sample diversity and across-sample heterogeneity of mutational signature activity in one or multiple populations of samples.
smoker_sigs_chen Activity of Smoking, APOBEC, and Ageing mutational signatures in a sample of East Asian lung adenocarcinoma patients.
smoker_sigs_chen_cossim Cosine similarity of smoking, APOBEC, and ageing mutational signatures found in a sample of East Asian lung adenocarcinoma patients.
time_weights Compute a normalized weighting vector based on a vector of sampling times.
TP53_context_counts_ordered Counts of each context class for the main transcript of gene TP53
TP53_drivers_intogen_LUAD Driver mutations from the intogen website for gene TP53 in lung adenocarcinomas
TP53_drivers_intogen_SBS96 SBS96 spectrum from the intogen website for gene TP53 in lung adenocarcinomas
zhang_sig_activity Activity of SBS mutational signatures in samples of lung cancer in never smokers
zhang_sig_similarity Cosine similarity of SBS mutational signatures found in samples of lung cancer in never smokers