Man pages for YAPSA
Yet Another Package for Signature Analysis
| 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_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_exposures_list_barplot | Plot the exposures of a cohort with different layers of... |
| annotation_heatmap_exposures | Heatmap to cluster the PIDs on their signature exposures... |
| 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_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_SMCs | Compare all strata from different stratifications |
| compare_to_catalogues | Compare one mutational catalogue to reference mutational... |
| complex_heatmap_exposures | Heatmap to cluster the PIDs on their signature exposures... |
| compute_comparison_stat_df | Extract statistical measures for entity comparison |
| computeLogLik | Compute the loglikelihood |
| confidence_indel_calulation | Wrapper to compute confidence intervals for SNV and INDEL... |
| confidence_indel_only_calulation | Wrapper to compute confidence intervals for only INDEL... |
| confIntExp | Compute confidence intervals |
| 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_mutation_catalogue_from_df | Wrapper to create an INDEL mutational catalog from a vlf-like... |
| create_indel_mut_cat_from_df | Create a Mutational catalog from a data frame |
| 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 |
| 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... |
| 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 |
| GenomeOfNl_raw | Example data for the Indel vignette |
| get_extreme_PIDs | Return those PIDs which have an extreme pattern for signature... |
| getSequenceContext | Extracts the sequence context up and downstream of a... |
| 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_SMC | CD stratification analysis |
| logLikelihood | Compute a loglikelihood ratio test |
| lymphomaNature2013_mutCat_df | Example mutational catalog for the SNV vignette |
| 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 |
| makeVRangesFromDataFrame | Construct a VRanges Object from a data frame |
| melt_exposures | Generically melts exposure data frames |
| merge_exposures | Merge exposure data frames |
| MutCat_indel_df | Example mutational catalog for the Indel vignette |
| normalize_df_per_dim | Useful functions on data frames |
| normalizeMotifs_otherRownames | Normalize Somatic Motifs with different rownames |
| plotExchangeSpectra | Plot the spectra of nucleotide exchanges |
| plotExchangeSpectra_indel | Plot the spectra of nucleotide exchanges of INDELs |
| plot_exposures | Plot the exposures of a cohort |
| plotExposuresConfidence | Plot exposures including confidence intervals |
| plotExposuresConfidence_indel | Plot exposures including confidence intervals for exposures... |
| plot_SMC | Plot results of the Stratification of a Mutational Catalogue |
| 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_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... |
| 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... |
| SMC | Stratification of a Mutational Catalogue |
| SMC_perPID | Run SMC at a per sample level |
| 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... |
| 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 |
| temp_trellis_rainfall_plot | Create a rainfall plot in a trellis structure |
| test_exposureAffected | Test significance of association |
| test_gene_list_in_exposures | Test if mutated PIDs are enriched in signatures |
| testSigs | Test for significance of alternative models cohort wide |
| 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 |
| trellis_rainfall_plot_old | Create a rainfall plot in a trellis structure |
| variateExp | Wrapper to compute confidence intervals for a cohort |
| variateExpSingle | Wrapper for the likelihood ratio test |
| YAPSA | Generate R documentation from inline comments. |
