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_heatmap_exposures | Heatmap to cluster the PIDs on their signature exposures... |

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_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... |

complex_heatmap_exposures | Heatmap to cluster the PIDs on their signature exposures... |

compute_comparison_stat_df | Extract statistical measures for entity comparison |

cosineDist | Compute the cosine distance of two vectors |

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. |

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... |

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 |

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 |

normalize_df_per_dim | Useful functions on data frames |

normalizeMotifs_otherRownames | Normalize Somatic Motifs with different rownames |

plotExchangeSpectra | Plot the spectra of nucleotide exchanges |

plot_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 |

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... |

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... |

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 |

YAPSA | Generate R documentation from inline comments. |

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