merge_homologues: Merge homologues

In polymapR: Linkage Analysis in Outcrossing Polyploids

Merge homologues

Description

Based on additional information, homologue fragments, separated during clustered should be merged again. merge_homologues allows to merge homologues per linkage group based on user input.

Usage

merge_homologues(LG_hom_stack, ploidy, LG, mergeList = NULL, log = NULL)

Arguments

LG_hom_stack	A data.frame with markernames, linkage group ("LG") and homologue ("homologue")
ploidy	The ploidy level of the plant species.
LG	The linkage group where the to be merged homologue fragments are in.
mergeList	A list of vectors of length 2, specifying the numbers of the homologue fragments to be merged. User input is asked if NULL.
log	Character string specifying the log filename to which standard output should be written. If NULL log is send to stdout.

Value

A modified LG_hom_stack

Examples

data("LGHomDf_P2_1")
merged<-merge_homologues(LGHomDf_P2_1,ploidy=4,LG=2,mergeList=list(c(1,5)))

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