LDbin: Create marker bins based on LD

In jendelman/MapRtools: Tools for genetic mapping

Create marker bins based on LD

Description

Create marker bins based on LD

Usage

LDbin(geno, r2.thresh = 0.99)

Arguments

geno	matrix of haplotype dosages (markers x indiv)
r2.thresh	threshold for binning

Details

Bins are created based on hierarchical clustering with hclust and method='single', using 1-r^2 as the dissimilarity metric. The argument r2.thresh controls the height for cutting the dendrogram to create the bins. The marker with the least missing data for each bin is chosen to represent it.

Value

List containing

bins

data frame with two columns: marker,bin

geno

genotype matrix for the bins

r2

r2 matrix for the bins

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