MutationalPatterns      MutationalPatterns: an integrative R package
                        for studying patterns in base substitution
                        catalogues
bin_mutation_density    Bin the genome based on mutation density
binomial_test           Binomial test for enrichment or depletion
                        testing
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
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.
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
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
mutation_context        Defunct functions in package
                        'MutationalPattern'
mutations_from_vcf      Retrieve base substitutions from vcf
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,region_cossim-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_occurrences      Count occurrences per base substitution type
                        and strand
type_context            Retrieve context of base substitution types
