# Yet Another Package for Signature Analysis

## Documentation for package ‘YAPSA’ version 1.4.0

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

## Help Pages

YAPSA-package | 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
AlexCosmicArtif_sigInd_df | Data for mutational signatures
AlexCosmicArtif_sig_df | Data for mutational signatures
AlexCosmicValid_sigInd_df | Data for mutational signatures
AlexCosmicValid_sig_df | Data for mutational signatures
AlexInitialArtif_sigInd_df | Data for mutational signatures
AlexInitialArtif_sig_df | Data for mutational signatures
AlexInitialValid_sigInd_df | Data for mutational signatures
AlexInitialValid_sig_df | Data for mutational signatures
annotate_intermut_dist_cohort | Annotate the intermutation distance of variants cohort-wide
annotate_intermut_dist_PID | Annotate the intermutation distance of variants per PID
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
average_over_present | Useful functions on data frames
build_gene_list_for_pathway | Build a gene list for a given pathway name
chosen_AlexInitialArtif_sigInd_df | Test and example data
chosen_signatures_indices_df | Test and example data
compare_exposures | Compares alternative exposures
compare_sets | Compare two sets of signatures by cosine distance
compare_SMCs | Compare all strata from different stratifications
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
COSMIC_subgroups_df | Test and example data
create_mutation_catalogue_from_df | Create a Mutational Catalogue from a data frame
create_mutation_catalogue_from_VR | Create a Mutational Catalogue from a VRanges Object
cutoffCosmicArtif_abs_df | Cutoffs for a supervised analysis of mutational signatures.
cutoffCosmicArtif_rel_df | Cutoffs for a supervised analysis of mutational signatures.
cutoffCosmicValid_abs_df | Cutoffs for a supervised analysis of mutational signatures.
cutoffCosmicValid_rel_df | Cutoffs for a supervised analysis of mutational signatures.
cutoffInitialArtif_abs_df | Cutoffs for a supervised analysis of mutational signatures.
cutoffInitialArtif_rel_df | Cutoffs for a supervised analysis of mutational signatures.
cutoffInitialValid_abs_df | Cutoffs for a supervised analysis of mutational signatures.
cutoffInitialValid_rel_df | Cutoffs for a supervised analysis of mutational signatures.
cutoffs | Cutoffs for a supervised analysis of mutational signatures.
cut_breaks_as_intervals | Wrapper for cut
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
LCD | Linear Combination Decomposition
LCD_complex_cutoff | LCD with a signature-specific cutoff on exposures
LCD_complex_cutoff_perPID | LCD with a signature-specific cutoff on exposures
lymphoma_Nature2013_COSMIC_cutoff_exposures_df | Test and example data
lymphoma_Nature2013_raw_df | Test and example data
lymphoma_PID_df | Test and example data
lymphoma_test_df | Test and example data
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_exposures | Plot the exposures of a cohort
plot_relative_exposures | Plot the exposures of a cohort
plot_SMC | Plot results of the Stratification of a Mutational Catalogue
plot_strata | Plot all strata from different stratification axes together
rel_lymphoma_Nature2013_COSMIC_cutoff_exposures_df | Test and example data
repeat_df | Create a data frame with default values
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'
run_SMC | Wrapper function for the Stratification of a Mutational Catalogue
sd_over_present | Useful functions on data frames
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
stderrmean_over_present | Useful functions on data frames
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_deconstructSigs_to_YAPSA | Change rownames from one naming convention to another
transform_rownames_MATLAB_to_R | Change rownames from one naming convention to another
transform_rownames_nature_to_R | Change rownames from one naming convention to another
transform_rownames_R_to_MATLAB | Change rownames from one naming convention to another
transform_rownames_YAPSA_to_deconstructSigs | Change rownames from one naming convention to another
translate_to_1kG | Translate chromosome names to the hg19 naming convention
translate_to_hg19 | Translate chromosome names to the hg19 naming convention
trellis_rainfall_plot | Create a rainfall plot in a trellis structure
YAPSA | Generate R documentation from inline comments.