buildMap | R Documentation |
Implements different algorithms for detecting linkage groups and ordering markers in each linkage group.
buildMap( res, opt.index, min.m = NULL, use.comu = FALSE)
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. |
This function determines linkage groups and order markers within each linkage group for class "netgwasmap".
An object with S3 class "netgwasmap"
is returned:
map |
Constructed linkage map associated with |
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 |
man |
stays TRUE. |
Pariya Behrouzi and Ernst C.Wit
Maintainer: Pariya Behrouzi pariya.behrouzi@gmail.com
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.
netmap
## 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)
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