Comprehensive genome-wide analysis of mutational processes


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Documentation for package ‘MutationalPatterns’ version 3.18.0

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MutationalPatterns-package MutationalPatterns: an integrative R package for studying patterns in base substitution catalogues
binomial_test Binomial test for enrichment or depletion testing
bin_mutation_density Bin the genome based on mutation density
calculate_lesion_segregation Calculate the amount of lesion segregation for a GRangesList or GRanges object.
cluster_signatures Signature clustering function
context_potential_damage_analysis Potential damage analysis for the supplied mutational contexts
convert_sigs_to_ref Convert tissue specific signature exposures to reference
cos_sim Cosine similarity function
cos_sim_matrix Compute all pairwise cosine similarities between mutational profiles/signatures
count_dbs_contexts Count DBS contexts
count_indel_contexts Count indel contexts
count_mbs_contexts Count MBS variants grouped by length.
determine_regional_similarity Determine regional mutation pattern similarity
enrichment_depletion_test Test for enrichment or depletion of mutations in genomic regions
explained_by_signatures Defunct functions in package 'MutationalPattern'
extract_signatures Extract mutational signatures from 96 mutation matrix using NMF
fit_to_signatures Find optimal nonnegative linear combination of mutation signatures to reconstruct the mutation matrix.
fit_to_signatures_bootstrapped Fit mutational signatures to a mutation matrix with bootstrapping
fit_to_signatures_strict Fit mutational signatures to a mutation matrix with less overfitting
genomic_distribution Find overlaps between mutations and a genomic region.
get_dbs_context Get DBS context
get_indel_context Get indel contexts
get_known_signatures Get known signatures
get_mut_type Get variants with mut_type from GRanges
get_sim_tb An S4 generic to get the sim_tb from a region_cossim object.
get_sim_tb-method An S4 generic to get the sim_tb from a region_cossim object.
lengthen_mut_matrix Lengthen mutation matrix
merge_signatures Merge signatures based on cosine similarity
MutationalPatterns MutationalPatterns: an integrative R package for studying patterns in base substitution catalogues
mutations_from_vcf Retrieve base substitutions from vcf
mutation_context Defunct functions in package 'MutationalPattern'
mutation_types Defunct functions in package 'MutationalPattern'
mut_192_occurrences Count 192 trinucleotide mutation occurrences
mut_96_occurrences Count 96 trinucleotide mutation occurrences
mut_context Retrieve context of base substitutions
mut_matrix Make mutation count matrix of 96 trinucleotides
mut_matrix_stranded Make mutation count matrix of 96 trinucleotides with strand information
mut_strand Find strand of mutations
mut_type Retrieve base substitution types from a VCF object
mut_type_occurrences Count the occurrences of each base substitution type
plot_192_profile Plot 192 trinucleotide profile
plot_96_profile Plot 96 trinucleotide profile
plot_bootstrapped_contribution Plot the bootstrapped signature contributions
plot_compare_dbs Compare two DBS mutation profiles
plot_compare_indels Compare two indel mutation profiles
plot_compare_mbs Compare two mbs mutation profiles
plot_compare_profiles Compare two 96 mutation profiles
plot_contribution Plot signature contribution barplot
plot_contribution_heatmap Plot signature contribution heatmap
plot_correlation_bootstrap Plots the correlation between bootstrapped signature contributions
plot_cosine_heatmap Plot cosine similarity heatmap
plot_dbs_contexts Plot the DBS contexts
plot_enrichment_depletion Plot enrichment/depletion of mutations in genomic regions
plot_indel_contexts Plot the indel contexts
plot_lesion_segregation Plot the strands of variants to show lesion segregation
plot_main_dbs_contexts Plot the main DBS contexts
plot_main_indel_contexts Plot the main indel contexts
plot_mbs_contexts Plot the MBS contexts
plot_original_vs_reconstructed Plot the similarity between a mutation matrix and its reconstructed profile
plot_profile_heatmap Plot a mutation matrix as a heatmap
plot_profile_region Plot 96 trinucleotide profile per subgroup
plot_rainfall Plot genomic rainfall
plot_regional_similarity Plot regional similarity
plot_river Plot a riverplot
plot_signature_strand_bias Plot signature strand bias
plot_spectrum Plot point mutation spectrum
plot_spectrum_region Plot point mutation spectrum per genomic region
plot_strand Plot strand per base substitution type
plot_strand_bias Plot strand bias per base substitution type per group
pool_mut_mat Pool multiple samples from a mutation matrix together
read_vcfs_as_granges Read VCF files into a GRangesList
region_cossim-class An S4 class to store the results of a regional mutation pattern similarity analysis
rename_nmf_signatures Rename NMF signatures based on previously defined signatures
show-method An S4 method to show an instance of the region_cossim class.
signature_potential_damage_analysis Potential damage analysis for the supplied mutational signatures
split_muts_region Split GRangesList or GRanges based on a list of regions.
strand_bias_test Significance test for strand asymmetry
strand_from_vcf Defunct functions in package 'MutationalPattern'
strand_occurrences Count occurrences per base substitution type and strand
type_context Retrieve context of base substitution types