Man pages for reimandlab/RM2
Regression Models For Localised Mutations
| dot-count_trinuc_muts | Counts number of mutations per quadnucleotide context |
| dot-get_all_trinucs | Return possible pyrimidine-centered trinucleotide contexts |
| dot-get_quadnuc_map | Determines all trinucleotide, pyrimidine-centered... |
| dot-get_trinucs2 | Counts the number of each trinucleotide within each site |
| dot-maf_to_dfr2 | Combines sites and mutations for sites and flanks from each... |
| dot-merge_sites_and_muts | Combines quadnucleotide counts and site information |
| dot-predict_muts_ranges_probs | Extract expected mutations count estimates by probability... |
| dot-prepare_bins_of_sites | Generates bins and calls prepare_sites such that site... |
| dot-prepare_sites2 | Get merged and trimmed sites and flanking regions and... |
| dot-shall_it_pass | Determines whether error is permitted |
| dot-split_seq_trinucs | Extract trinucleotides from sequence |
| dot-test_NB_model | Runs negative binomial regression and likelihood ratio test |
| dot-trim_chrom_boundaries | Clean sites near chromosome boundaries |
| dot-which_median | Selects median value with priority given to larger value |
| get_mutations_in_flanked_sites | Mutation counts along relative positions |
| get_mut_trinuc_strand | Derive quadnucleotide contexts, strandedness and single-base... |
| plot_mutations_in_flanked_sites | Visualize mutations in sites and flanks |
| RM2 | Regression models for localised mutations: Evaluating... |
| RM2_downsample | Evaluating differential mutation rates across classes of... |
