GenomeOfNl_raw          Example data for the Indel vignette
LCD                     Linear Combination Decomposition
LCD_SMC                 CD stratification analysis
LCD_complex_cutoff      LCD with a signature-specific cutoff on
                        exposures
MutCat_indel_df         Example mutational catalog for the Indel
                        vignette
SMC                     Stratification of a Mutational Catalogue
SMC_perPID              Run SMC at a per sample level
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_exposures_list_barplot
                        Plot the exposures of a cohort with different
                        layers of annotation for SNV and INDEL
                        signatures
annotation_heatmap_exposures
                        Heatmap to cluster the PIDs on their signature
                        exposures (ComplexHeatmap)
attribute_nucleotide_exchanges
                        Attribute the nucleotide exchange for an SNV
attribute_sequence_contex_indel
                        Attribution of sequence context and size for an
                        INDEL
attribution_of_indels   Attribution of variant into one onf the 83
                        INDEL categories
build_gene_list_for_pathway
                        Build a gene list for a given pathway name
classify_indels         INDEL function V1 - not compartible with
                        AlexandrovSignatures
compare_SMCs            Compare all strata from different
                        stratifications
compare_exposures       Compares alternative exposures
compare_expousre_sets   Compare two sets of exposures by cosine
                        distance
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)
computeLogLik           Compute the loglikelihood
compute_comparison_stat_df
                        Extract statistical measures for entity
                        comparison
confIntExp              Compute confidence intervals
confidence_indel_calulation
                        Wrapper to compute confidence intervals for SNV
                        and INDEL signatures of a cohort or
                        single-sample
confidence_indel_only_calulation
                        Wrapper to compute confidence intervals for
                        only INDEL signatures.
correct_rounded         Readjust the vector to it's original norm after
                        rounding
cosineDist              Compute the cosine distance of two vectors
cosineMatchDist         Compute an altered cosine distance of two
                        vectors
create_indel_mut_cat_from_df
                        Create a Mutational catalog from a data frame
create_indel_mutation_catalogue_from_df
                        Wrapper to create an INDEL mutational catalog
                        from a vlf-like data frame
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.
cutoffs_pcawg           Opt. cutoffs, PCAWG SNV signatures, including
                        artifacts
deriveSigInd_df         Derive a signature_indices_df object
disambiguateVector      Disambiguate a vector
enrichSigs              Compare to background distribution
exampleINDEL_YAPSA      Data structures used in examples, Indel tests
                        and the Indel signature vignette of the YAPSA
                        package.
exampleYAPSA            Test and example data
exchange_colour_vector
                        Colours codes for displaying SNVs
exome_mutCatRaw_df      Example mutational catalog for the exome
                        vignette
exposures_barplot       Wrapper for enhanced_barplot
extract_names_from_gene_list
                        Return gene names from gene lists
find_affected_PIDs      Find samples affected
getSequenceContext      Extracts the sequence context up and downstream
                        of a nucleotide position
get_extreme_PIDs        Return those PIDs which have an extreme pattern
                        for signature exposure
hclust_exposures        Cluster the PIDs according to their signature
                        exposures
logLikelihood           Compute a loglikelihood ratio test
lymphomaNature2013_mutCat_df
                        Example mutational catalog for the SNV vignette
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
plotExchangeSpectra_indel
                        Plot the spectra of nucleotide exchanges of
                        INDELs
plotExposuresConfidence
                        Plot exposures including confidence intervals
plotExposuresConfidence_indel
                        Plot exposures including confidence intervals
                        for exposures of SNVs and INDELs
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
read_entry              Read a single vcf-like file into a single data
                        frame
relateSigs              Make unique assignments between sets of
                        signatures
repeat_df               Create a data frame with default values
round_precision         Round to a defined precision
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
sigs_pcawg              Data for PCAWG SNV signatures (COSMIC v3),
                        including artifacts
                        'PCAWG_SP_SBS_sigs_Artif_df': Data frame of the
                        signatures published by Alexandrov et al.
                        (Biorxiv 2013) which were decomposed with the
                        method SigProfiler. SNV signatures are labeled
                        with SBS, single base signature. There are 67
                        signatures which constitute the columns, 47 of
                        which were validated by a bayesian NFM mehtod,
                        SignatureAnayzer. Validated signatures are
                        SBS1-SBS26,SBS28-SBS42 and SBS44. SBS7 is split
                        up into 7 a/b/c and d. SBS10 ans SBS17 are both
                        split up into a and b. Resulting in a 47
                        validated sigantures. Please note, unlike the
                        paper by Alexandrov et al. (Biorxiv 2018) the
                        data sets do not contain a SBS84 and SBS85 as
                        not all were availiablt to perfom supervised
                        signature analysis. In total there are 96
                        different features and therefore 96 rows when
                        dealing with a trinucleotide context.
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
testSigs                Test for significance of alternative models
                        cohort wide
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
variateExp              Wrapper to compute confidence intervals for a
                        cohort
variateExpSingle        Wrapper for the likelihood ratio test
