onemap (version 3.0.0)

group_upgma: 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)

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.

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)

Author

Marcelo Mollinari,

Cristiane Taniguti

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_. tools:::Rd_expr_doi("10.1534/g3.119.400378")

Examples

# \donttest{
 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)
# }