mpgroup: Construct linkage groups using 2-point recombination fraction...
In behuang/mpMap: Multi-Parent RIL Genetic Analysis

Description Usage Arguments Value Examples

Use two-point recombination fraction estimates to group markers into the specified number of linkage group, The input initial can be used to select groups of markers that will be assigned to the same group. Grouping is performed using hierarchical clustering (hclust) using either average, complete or single linkage. The matrix used for clustering can be either theta (the recombination fraction matrix), lod (the log likelihood ratio) or a combination of the two.

1 2	mpgroup(mpcross, groups, initial = NULL, clusterBy = "combined", method = "average")

`mpcross`	Object of class `mpcross`
`groups`	The number of groups to be formed
`initial`	A list, with each entry containing markers which are to be assigned to the same group. Markers can be referenced by name or by index
`clusterBy`	The type of data to cluster by. Can be one of "theta" for recombination fraction, "lod" for log likelihood ration, or "combined" for a combination of the two
`method`	The clustering method to use. Must be one of "single", "complete" or "average"

A copy of the input mpcross object, with an additional "lg" entry containing the groupings of the markers. In addition the recombination fraction estimates and genetic data are reordered according to the created groupings of markers.

`lg$groups`	Numeric vector giving the group to which each marker belongs
`lg$all.groups`	Numeric vector giving the numbers for any groups that are present

map <- qtl::sim.map(len=rep(100, 2), n.mar=11, eq.spacing=TRUE, include.x=FALSE)
sim.ped <- sim.mpped(4, 1, 500, 6, 1)
sim.dat <- sim.mpcross(map=map, pedigree=sim.ped, 
	qtl=matrix(data=c(1, 50, .4, 0, 0, 0), 
	nrow=1, ncol=6, byrow=TRUE), seed=1)
dat.rf <- mpestrf(sim.dat)
grouped <- mpgroup(dat.rf, groups=2, clusterBy="combined", method="average")
grouped$lg