recomb_map_inds: Map recombination breaks from genetic positions to base pair...

In simfam: Simulate and Model Family Pedigrees with Structured Founders

Map recombination breaks from genetic positions to base pair coordinates

Description

Given a list of individuals with recombination breaks given in genetic distance (such as the output of recomb_fam()), and a genetic map (see recomb_map_hg), this function determines all positions in base pair coordinates. If base pair positions existed in input, they are overwritten.

Usage

recomb_map_inds(inds, map)

Arguments

inds	The list of individuals, each of which is a list with two haploid individuals named pat and mat, each of which is a list of chromosomes (always identified by number, but may also be named arbitrarily), each of which is a data.frame/tibble with implicit ranges (posg is end coordinates in cM; start is the end of the previous block, zero for the first block) and ancestors anc as strings.
map	The genetic map, a list of chromosomes each of which is a data.frame/tibble with columns pos for base pair position and posg for genetic position.

Details

Genetic positions are converted to base pair positions from the provided map using linear interpolation, using stats::approx() with options rule = 2 (out of range cases are set to nearest end's value) and ties = list( 'ordered', mean ) (assume data is ordered, interpolate ties in genetic distance in map using mean of base pair positions). Output will be incorrect, without throwing errors, if genetic map is not ordered. Base pair positions are rounded to integers.

Value

The input list of individuals, with each chromosome added column pos corresponding to end coordinate in base pairs. Each chromosome has columns reordered so pos, posg, and anc appear first, and any additional columns appear afterwards.

See Also

recomb_fam() for drawing recombination breaks of individuals from a pedigree.

recomb_map_hg for simplified human recombination maps included in this package.

Examples

# Lengthy code creates individuals with recombination data to map
# The smallest pedigree, two parents and a child (minimal fam table).
library(tibble)
fam <- tibble(
  id = c('father', 'mother', 'child'),
  pat = c(NA, NA, 'father'),
  mat = c(NA, NA, 'mother')
)
# use latest human recombination map, but just first two chrs to keep this example fast
map <- recomb_map_hg38[ 1:2 ]
# initialize parents with this other function
founders <- recomb_init_founders( c('father', 'mother'), map )
# draw recombination breaks for child
inds <- recomb_fam( founders, fam )

# now use this function to add base pair coordinates for recombination breaks!
inds <- recomb_map_inds( inds, map )

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