dot-prepare_bins_of_sites: Generates bins and calls prepare_sites such that site...

In reimandlab/RM2: Regression Models For Localised Mutations

Generates bins and calls prepare_sites such that site coordinates, number of trinucleotide contexts and indels, and all possible quadnucleotide contexts are returned for each mutation rate bin and site + flank

Description

Generates bins and calls prepare_sites such that site coordinates, number of trinucleotide contexts and indels, and all possible quadnucleotide contexts are returned for each mutation rate bin and site + flank

Usage

.prepare_bins_of_sites(
  sites,
  window_size,
  maf,
  n_bin = NA,
  n_min_mut = 100,
  global_mut_rate_window = 1e+06
)

Arguments

sites	Data frame of sites
window_size	Integer indicating the half-width of sites and flanking regions
maf	Data frame of mutations prepared by get_mut_trinuc_strand
n_bin	Integer (default 10) indicating the number of bins to which to split sites
n_min_mut	Integer (default 100) indicating minimum number of mutations to proceed with analysis
global_mut_rate_window	Integer (default 1e6) indicating the window for mutation rate binning

Value

List of length n_bin each containing two GRanges of coordinates (site and flanks) and two dataframes of trinucleotide counts and mutation contexts

reimandlab/RM2 documentation built on Aug. 13, 2022, 12:22 p.m.