buildMap {netgwas}

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, min.m = NULL, use.comu = FALSE)

Arguments

res

An object with S3 class "netgwasmap"

opt.index

An index of a desired regularization parameter.

min.m

Expected minimum number of markers in a chromosome. Optional

use.comu

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

Details

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

Value

An object with S3 class "netgwasmap" is returned:

map

Constructed linkage map associated with opt.index.

opt.index

The index of a desired 3-D map to construct linkage map.

cross

The specified cross type by user.

allres

A list containing results for different regularization parameter. Belongs to class "netgwas". To visualize a path of different 3D maps consider function plot.netgwas. Note that the input data is reordered based on the estimated linkage map and is saved as data in this argument.

man

stays TRUE.

Author(s)

Pariya Behrouzi and Ernst C.Wit
Maintainer: Pariya Behrouzi [e-mail]

References

1. Behrouzi, P., and Wit, E. C. (2018). De novo construction of polyploid linkage maps using discrete graphical models. Bioinformatics.
2. Behrouzi, P., and Wit, E. C. (2017c). netgwas: An R Package for Network-Based Genome-Wide Association Studies. arXiv preprint, arXiv:1710.01236.

See Also

netmap

Examples

## Not run: 
data(CviCol)
#Randomly change the order of markers across the genome
cvicol <- CviCol[ ,sample(ncol(CviCol))]

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

#Visualization of other networks
plot(out$allres)  
#Constructing a linkage map for 5th network
bm <- buildMap(out, opt.index=5); bm
plot(bm, vis= "summary")
#or
plot(bm, vis= "interactive", label.vertex="all")

## End(Not run)