Description Usage Arguments Value See Also
Groups markers based on estimated pairwise recombination fractions. Linkage groups are built up by adding a marker if it satisfies the criteria for linkage with at least one other marker in the group.
1 |
mpcross |
an object of class |
theta |
Threshold for grouping based on recombination fraction value |
LOD |
Threshold for grouping based on LOD score value |
The original object, with the added component lg
which is a list with the following components:
n.groups |
The number of linkage groups formed by the function |
groups |
Vector labelling each marker by assigned linkage group. Missing values mean that the marker was linked to more than one group and could not be assigned with confidence |
LODthresh |
The LOD threshold value used to determine linkage |
thetathresh |
The theta threshold value used to determine linkage |
order |
A list with a component for each constructed linkage group which contains the order of the markers within the linkage group |
map <- sim.map(len=100, 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) dat.lg <- mpgroup(dat.rf)
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