MutationalPatterns-package | MutationalPatterns: an integrative R package for studying patterns in base substitution catalogues |
binomial_test | Binomial test for enrichment or depletion testing |
cluster_signatures | Signature clustering function |
cos_sim | Cosine similarity function |
cos_sim_matrix | Compute all pairwise cosine similarities between mutational profiles/signatures |
enrichment_depletion_test | Test for enrichment or depletion of mutations in genomic regions |
explained_by_signatures | This function has been renamed to 'cos_sim_matrix'. |
extract_signatures | Extract mutational signatures from 96 mutation matrix using NMF |
fit_to_signatures | Find optimal nonnegative linear combination of mutation signatures to reconstruct the mutation matrix. |
genomic_distribution | Find overlaps between mutations and a genomic region. |
MutationalPatterns | MutationalPatterns: an integrative R package for studying patterns in base substitution catalogues |
mutations_from_vcf | Retrieve base substitutions from vcf |
mutation_context | This function has been removed. Use 'mut_context' instead. |
mutation_types | This function has been renamed. Use 'mut_type' instead. |
mut_context | Retrieve context of base substitutions |
mut_matrix | Make mutation count matrix of 96 trinucleotides |
mut_matrix_stranded | Make mutation count matrix of 96 trinucleotides with strand information |
mut_strand | Find strand of mutations |
mut_type | Retrieve base substitution types from a VCF object |
mut_type_occurrences | Count the occurrences of each base substitution type |
plot_192_profile | Plot 192 trinucleotide profile |
plot_96_profile | Plot 96 trinucleotide profile |
plot_compare_profiles | Compare two 96 mutation profiles |
plot_contribution | Plot signature contribution barplot |
plot_contribution_heatmap | Plot signature contribution heatmap |
plot_cosine_heatmap | Plot cosine similarity heatmap |
plot_enrichment_depletion | Plot enrichment/depletion of mutations in genomic regions |
plot_rainfall | Plot genomic rainfall |
plot_signature_strand_bias | Plot signature strand bias |
plot_spectrum | Plot point mutation spectrum |
plot_strand | Plot strand per base substitution type |
plot_strand_bias | Plot strand bias per base substitution type per group |
read_vcfs_as_granges | Read VCF files into a GRangesList |
strand_bias_test | Significance test for strand asymmetry |
strand_from_vcf | This function has been renamed. Use 'mut_strand' instead. |
strand_occurrences | Count occurrences per base substitution type and strand |
type_context | Retrieve context of base substitution types |