group_mappoly | R Documentation |
Identifies linkage groups of markers using the results of two-point (pairwise) analysis.
group_mappoly( input.mat, expected.groups = NULL, inter = TRUE, comp.mat = FALSE, LODweight = FALSE, verbose = TRUE )
input.mat |
an object of class |
expected.groups |
when available, inform the number of expected linkage groups (i.e. chromosomes) for the species |
inter |
if |
comp.mat |
if |
LODweight |
if |
verbose |
logical. If |
Returns an object of class mappoly.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 |
chisq.pval.thres |
the threshold used on the segregation test when reading the dataset |
chisq.pval |
the p-values associated with the segregation test for all markers in the sequence |
Marcelo Mollinari, mmollin@ncsu.edu
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
## Getting first 20 markers from two linkage groups all.mrk <- make_seq_mappoly(hexafake, c(1:20,601:620)) red.mrk <- elim_redundant(all.mrk) unique.mrks <- make_seq_mappoly(red.mrk) counts <- cache_counts_twopt(unique.mrks, cached = TRUE) all.pairs <- est_pairwise_rf(input.seq = unique.mrks, count.cache = counts, ncpus = 1, verbose = TRUE) ## Full recombination fraction matrix mat.full <- rf_list_to_matrix(input.twopt = all.pairs) plot(mat.full, index = FALSE) lgs <- group_mappoly(input.mat = mat.full, expected.groups = 2, inter = TRUE, comp.mat = TRUE, #this data has physical information verbose = TRUE) lgs plot(lgs)
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.