split_linkage_info: Split linkage information into homologues

In mdavy86/polymapR: Linkage Analysis in Outcrossing Polyploids

Description

After running finish_linkage_analysis recombination frequency, LOD and phase are grouped by linkage group. This functions classifies them into homologue within the linkage group.

Usage

split_linkage_info(all_linkages, marker_assignment, ploidy, log = NULL)

Arguments

all_linkages	A list of linkage information divided by linkage group as output of finish_linkage_analysis.
marker_assignment	A complete marker assignment data.frame containing all markers.
ploidy	Integer. The ploidy level of the plant species.
log	Character string specifying the log filename to which standard output should be written. If NULL log is send to stdout.

Value

A nested list with linkage group on the first level and homologue on the second.

Examples

data("marker_assignments_P1", "all_linkages_list_P1")
splitted_list<-split_linkage_info(all_linkages_list_P1, marker_assignments_P1, 4)

mdavy86/polymapR documentation built on May 25, 2019, 9:35 p.m.