group_upgma: Assign markers to linkage groups

In onemap: Construction of Genetic Maps in Experimental Crosses

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, [e-mail]

Cristiane Taniguti [e-mail]

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_. \Sexpr[results=rd]{tools:::Rd_expr_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 June 8, 2025, 1:55 p.m.