LGtrim: Trim a linkage group based on genotype frequencies

In jendelman/MapRtools: Tools for genetic mapping

Trim a linkage group based on genotype frequencies

Description

Trim a linkage group based on genotype frequencies

Usage

LGtrim(geno, LODmat, thresh)

Arguments

geno	matrix of haplotype dosages (markers x samples)
LODmat	matrix of LOD scores for the markers
thresh	numeric vector of thresholds for clusterings

Details

This function should only be run on a single linkage group (to form the linkage groups, use LG. If thresh is a numeric vector with multiple LOD thresholds, the function returns a plot showing the impact of the threshold on genotype frequencies. If thresh is a single value, the function returns a vector of the marker names that are retained. The rownames of geno and LODmat must match.

Value

Either a ggplot2 object or a vector of marker names (see Details)

jendelman/MapRtools documentation built on April 12, 2025, 12:46 p.m.