group_upgma function

Assign markers to linkage groups

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.

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)

Returns

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.

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)

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")

Author(s)

Marcelo Mollinari, mmollin@ncsu.edu

Cristiane Taniguti chtaniguti@tamu.edu