id_recombination_events: Identify crossover points from state sequences and snp...

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

This is a simple function that takes a vector of parental states along a chromosome and identifies where states have changed.

Usage

id_recombination_events(snps_genotypes_df)

Arguments

snps_genotypes_df

a data.frame with two columns: snps a vector of ordered snp locations (in bps) states a vector of corresponding inferred states, either haploid (2 states = 0 or 1) or diploid with three states possible (0,1,2)

Value

a data.frame containing the midpoint between focal snp i and snp i-1 and whether their states were the same (0) or different (1).

Author(s)

Tyler D. Hether

See Also

fb_haploid, fb_diploid

Examples

df <- data.frame(snps=100*(1:10),
   states=c(rep(0,4), rep(1,6)))
id_recombination_events(df)

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