# Comprehensive genome-wide analysis of mutational processes

## Documentation for package ‘MutationalPatterns’ version 3.22.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

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

A mutation_matrix calculated on a GRangesList or GR object modified by 'split_muts_region()', will contain a column per combination of sample and genomic region. In essence different regions are treated as different samples. This function will transform the matrix, so that these regions are instead treated as different mutation types. For example, instead of 'C[C>T]G', you might have the feature 'C[C>T]G Promoter'. The number of rows in the matrix will thus be multiplied by the number of regions. After using 'split_muts_region()', use 'mut_matrix()' to get a mut_matrix that can be used for this function. The result can be plotted with plot_profile_region, but could also be used for NMF, refitting ect.

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