buildMap: linkage group detection and ordering markers for class "netgwasmap"

Description

Implements different algorithms for detecting linkage groups and ordering markers in each linkage group.

Usage

buildMap( res, opt.index, num.iso.m = NULL, use.comu = FALSE)

Arguments

res

An object with S3 class "netgwasmap"

opt.index

An index of a desired regularization parameter.

num.iso.m

A number of unlinked markers to be counted as isolated markers. Default is one.

use.comu

Using community detection algorithm to detect linkage groups. Default is FALSE.

Value

map

An estimated linkage map for a graph G associated with the specified regularization parameter in opt.index

Details

This function determines linkage groups and order markers within each linkage group for class "netgwasmap".

References

1. Behrouzi, P., and Wit, E. C. (2017b). De novo construction of q-ploid linkage maps using discrete graphical models. arXiv preprint, arXiv:1710.01063. 2. Behrouzi, P., and Wit, E. C. (2017c). netgwas: An R Package for Network-Based Genome-Wide Association Studies. arXiv preprint, arXiv:1710.01236.

Examples

Run this code

# NOT RUN {
data(CviCol)
#Randomly change the order of markers across the genome
cvicol <- CviCol[ ,sample(1:ncol(CviCol), ncol(CviCol), replace=FALSE)]

#Constructing linkage map for Cvi x Col genotype data
out <- netmap(cvicol, cross.typ= "inbred", vis= FALSE, ncores=1); out
plot(out)
map <- out$map; map

#Visualization of other three-dimensional maps
plot(out$allres)  
#Constructing a linkage map for 5th three-dimensional map
bm <- buildMap(out, opt.index=5); bm
# }

Run the code above in your browser using DataCamp Workspace