LCD                     Linear Combination Decomposition
LCD_complex_cutoff      LCD with a signature-specific cutoff on
                        exposures
YAPSA                   Generate R documentation from inline comments.
add_annotation          Add information to an annotation data structure
add_as_fist_to_list     Add an element as first entry to a list
aggregate_exposures_by_category
                        Aggregate exposures by category
annotate_intermut_dist_PID
                        Annotate the intermutation distance of variants
                        per PID
annotate_intermut_dist_cohort
                        Annotate the intermutation distance of variants
                        cohort-wide
annotation_exposures_barplot
                        Plot the exposures of a cohort with different
                        layers of annotation
annotation_heatmap_exposures
                        Heatmap to cluster the PIDs on their signature
                        exposures (ComplexHeatmap)
attribute_nucleotide_exchanges
                        Attribute the nucleotide exchange for an SNV
build_gene_list_for_pathway
                        Build a gene list for a given pathway name
compare_SMCs            Compare all strata from different
                        stratifications
compare_exposures       Compares alternative exposures
compare_sets            Compare two sets of signatures by cosine
                        distance
compare_to_catalogues   Compare one mutational catalogue to reference
                        mutational catalogues
complex_heatmap_exposures
                        Heatmap to cluster the PIDs on their signature
                        exposures (ComplexHeatmap)
compute_comparison_stat_df
                        Extract statistical measures for entity
                        comparison
cosineDist              Compute the cosine distance of two vectors
create_mutation_catalogue_from_VR
                        Create a Mutational Catalogue from a VRanges
                        Object
create_mutation_catalogue_from_df
                        Create a Mutational Catalogue from a data frame
cut_breaks_as_intervals
                        Wrapper for cut
cutoffs                 Cutoffs for a supervised analysis of mutational
                        signatures.
exampleYAPSA            Test and example data
exchange_colour_vector
                        Colours codes for displaying SNVs
exposures_barplot       Wrapper for enhanced_barplot
extract_names_from_gene_list
                        Return gene names from gene lists
find_affected_PIDs      Find samples affected
get_extreme_PIDs        Return those PIDs which have an extreme pattern
                        for signature exposure
hclust_exposures        Cluster the PIDs according to their signature
                        exposures
makeVRangesFromDataFrame
                        Construct a VRanges Object from a data frame
make_catalogue_strata_df
                        Group strata from different stratification axes
make_comparison_matrix
                        Compute a similarity matrix for different
                        strata
make_strata_df          Group strata from different stratification axes
make_subgroups_df       Make a custom data structure for subgroups
melt_exposures          Generically melts exposure data frames
merge_exposures         Merge exposure data frames
normalizeMotifs_otherRownames
                        Normalize Somatic Motifs with different
                        rownames
normalize_df_per_dim    Useful functions on data frames
plotExchangeSpectra     Plot the spectra of nucleotide exchanges
plot_SMC                Plot results of the Stratification of a
                        Mutational Catalogue
plot_exposures          Plot the exposures of a cohort
plot_strata             Plot all strata from different stratification
                        axes together
repeat_df               Create a data frame with default values
run_SMC                 Wrapper function for the Stratification of a
                        Mutational Catalogue
run_annotate_vcf_pl     Wrapper function to annotate addition
                        information
run_comparison_catalogues
                        Compare all strata from different
                        stratifications
run_comparison_general
                        Compare all strata from different
                        stratifications
run_kmer_frequency_correction
                        Provide comprehensive correction factors for
                        kmer content
run_kmer_frequency_normalization
                        Provide normalized correction factors for kmer
                        content
run_plot_strata_general
                        Wrapper function for 'plot_strata'
shapiro_if_possible     Wrapper for Shapiro test but allow for all
                        identical values
sigs                    Data for mutational signatures
split_exposures_by_subgroups
                        Split an exposures data frame by subgroups
stat_plot_subgroups     Plot averaged signature exposures per subgroup
stat_test_SMC           Apply statistical tests to a stratification
                        (SMC)
stat_test_subgroups     Test for differences in average signature
                        exposures between subgroups
stderrmean              Compute the standard error of the mean
sum_over_list_of_df     Elementwise sum over a list of (numerical) data
                        frames
targetCapture_cor_factors
                        Correction factors for different target capture
                        kits
test_exposureAffected   Test significance of association
test_gene_list_in_exposures
                        Test if mutated PIDs are enriched in signatures
transform_rownames_R_to_MATLAB
                        Change rownames from one naming convention to
                        another
translate_to_hg19       Translate chromosome names to the hg19 naming
                        convention
trellis_rainfall_plot   Create a rainfall plot in a trellis structure
