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. |