recomb_map_fix_ends_chr: Extrapolate and shift recombination map of one chromosome to...

In simfam: Simulate and Model Family Pedigrees with Structured Founders

Extrapolate and shift recombination map of one chromosome to ends

Description

Given an existing recombination map and a chromosome length in base pairs, extrapolates the map to ensure all positions are covered, and shifts to ensure position one in basepairs corresponds to position 0 in genetic position. Recombination rates are extrapolated from the first and last 10Mb of data by default (separately per end). Therefore fixes the fact that common maps start genetic position zero at base pair position >> 1 and do not extend to ends (some SNPs from modern projects fall out of range without fixes).

Usage

recomb_map_fix_ends_chr(map, pos_length, pos_delta = 10000000L)

Arguments

map	A tibble with two columns: pos position in base pairs, and posg position in centiMorgans (cM).
pos_length	The length of the chromosome in base pairs.
pos_delta	The size of the window used to extrapolate recombination rates.

Value

The extrapolated recombination map, shifted so the first non-trivial position maps to the genetic distance expected from the extrapolated rate at the beginning, then added a first trivial position (pos=1, posg=0) and final basepair position at length of chromosome and expected genetic position from end extrapolation.

See Also

recomb_map_simplify_chr() to simplify recombination maps to a desired numerical accuracy.

Examples

library(tibble)
# create a toy recombination map with at least 10Mb at each end
map <- tibble(
    pos  = c( 3L,  15L, 100L, 120L ) * 1e6L,
    posg = c(  0, 10.4, 90.1,  110 )
)
# and length
pos_length <- 150L * 1e6L

# apply function!
map_fixed <- recomb_map_fix_ends_chr( map, pos_length )
# inspect
map_fixed

simfam documentation built on Jan. 10, 2023, 1:06 a.m.