get_mutations_in_flanked_sites: Mutation counts along relative positions
In reimandlab/RM2: Regression Models For Localised Mutations

get_mutations_in_flanked_sites

R Documentation

Mutation counts along relative positions

Prepares data frame of mutations at relative positions along flanks and sites

get_mutations_in_flanked_sites(mutations, this_sites, window_size, n_patients)

`mutations`	Data frame of mutations
`this_sites`	Data frame of sites
`window_size`	Integer indicating the half-width of sites and flanking regions (added to both sides of midpoint)
`n_patients`	Integer indicating number of patients

Data frame containing the frequency of mutations across site and flank positions

dist: the relative position of each base to nearest site midpoint
mut_count: the number of overlapping mutations
is_site: boolean indicating if the position is within the site
mut_freq: frequency of mutations calculated as mut_count / n_patients / total bp * 1e6