group_upgma: Assign markers to linkage groups
In onemap: Construction of Genetic Maps in Experimental Crosses

group_upgma

R Documentation

Assign markers to linkage groups

Description

Identifies linkage groups of markers using the results of two-point (pairwise) analysis and UPGMA method. Function adapted from MAPpoly package written by Marcelo Mollinari.

Usage

group_upgma(input.seq, expected.groups = NULL, inter = TRUE, comp.mat = FALSE)

Arguments

`input.seq`	an object of class `mappoly.rf.matrix`
`expected.groups`	when available, inform the number of expected linkage groups (i.e. chromosomes) for the species
`inter`	if `TRUE` (default), plots a dendrogram highlighting the expected groups before continue
`comp.mat`	if `TRUE`, shows a comparison between the reference based and the linkage based grouping, if the sequence information is available (default = FALSE)

Value

Returns an object of class group, which is a list containing the following components:

`data.name`	the referred dataset name
`hc.snp`	a list containing information related to the UPGMA grouping method
`expected.groups`	the number of expected linkage groups
`groups.snp`	the groups to which each of the markers belong
`seq.vs.grouped.snp`	comparison between the genomic group information (when available) and the groups provided by `group_upgma`
`LOD`	minimum LOD Score to declare linkage.
`max.rf`	maximum recombination fraction to declare linkage.
`twopt`	name of the object of class `rf.2ts` used as input, i.e., containing information used to assign markers to linkage groups.

Author(s)

Marcelo Mollinari, mmollin@ncsu.edu

Cristiane Taniguti chtaniguti@tamu.edu

References

Mollinari, M., and Garcia, A. A. F. (2019) Linkage analysis and haplotype phasing in experimental autopolyploid populations with high ploidy level using hidden Markov models, _G3: Genes, Genomes, Genetics_. doi: 10.1534/g3.119.400378

Examples


 data("vcf_example_out")
 twopts <- rf_2pts(vcf_example_out)
 input.seq <- make_seq(twopts, "all")
 lgs <- group_upgma(input.seq, expected.groups = 3, comp.mat=TRUE, inter = FALSE)
 plot(lgs)

onemap documentation built on Nov. 26, 2022, 9:05 a.m.