getLinkedPairs {KLINK}

Identify linked marker pairs

Description

This function returns a "maximal" set of disjoint pairs of linked markers, given a genetic marker map and a subset of the markers included in the map. The pairs are identified in a greedy manner, successively choosing the closest markers on each chromosome.

Usage

getLinkedPairs(markers, linkageMap, maxdist = Inf)

Arguments

markers

A character vector containing marker names.

linkageMap

A data frame with columns including Marker, Chrom and PosCM.

maxdist

A positive number indicating the maximum linkage distance (in cM). Markers further apart than this are considered unlinked.

Value

A list of character vectors, each containing two marker names.

Examples

# Example using the built-in map of 50 STR markers
map = KLINK::LINKAGEMAP

getLinkedPairs(map$Marker, map, maxdist = 25)