recombine_index: Simulate recombination points along a chromosome.

In tylerhether/HMMancestry: R package using the Forward-Backward algorithm to infer genotypes, recombination hotspots, and gene conversion tracts from low-coverage next-generation sequence data

Description

Simulate recombination events given the vector of snp locations and recombination rate(s). Haldane's function is used to simulate the probabilty of getting an odd number of crossover events between any two snps given their physical distance and the specified recombination rate.

Usage

recombine_index(scale, snps)

Arguments

scale	either vector of length 1 specifying the genome-wide recombination rate (Morgans/bp) or a vector of length snps-1 specifying the recombination rate between all snps. In either case rates must be positive.
snps	a vector gving the locations of snps along a chromosome

Value

a vector of length snps-1 specifying the location of recombiantion points.

Author(s)

Tyler D. Hether

See Also

make_parents

Examples

set.seed(1234567)
# Simulating recombination across 1000 loci randomly spaced
# along a 200kbp chromosome
chromSize <- 2e5 		# Chromosome size
l <- 1e3 				# number of loci to simulate
c <- 1e-04 				# Morgans/bp
snps <- sort(sample(size=l, 1:chromSize, replace=FALSE))
# Find recombination points between all the snps
recomb_points <- recombine_index(scale=c, snps=snps)
recomb_points

tylerhether/HMMancestry documentation built on May 3, 2019, 1:53 p.m.