define_LG_structure: Generate linkage group and homologue structure of SxN markers

In polymapR: Linkage Analysis in Outcrossing Polyploids

Generate linkage group and homologue structure of SxN markers

Description

Function which organises the output of cluster_SN_markers into a data frame of numbered linkage groups and homologues. Only use this function if it is clear from the graphical output of cluster_SN_markers that there are LOD scores present which define both chromosomes (lower LOD) and homologues (higher LOD).

Usage

define_LG_structure(cluster_list, LOD_chm, LOD_hom, LG_number, log = NULL)

Arguments

cluster_list	A list of cluster_stacks, the output of cluster_SN_markers.
LOD_chm	Integer. The LOD threshold specifying at which LOD score the markers divide into chromosomal groups
LOD_hom	Integer. The LOD threshold specifying at which LOD score the markers divide into homologue groups
LG_number	Integer. Expected number of chromosomes (linkage groups). Note that if this number of clusters are not present at LOD_chm, the function will abort.
log	Character string specifying the log filename to which standard output should be written. If NULL log is send to stdout.

Value

A data.frame with markers classified by homologue and linkage group.

Examples

data("P1_homologues")
ChHomDf<-define_LG_structure(cluster_list=P1_homologues,LOD_chm=3.5,LOD_hom=5,LG_number=5)

polymapR documentation built on Nov. 5, 2023, 1:09 a.m.