mpadd: Add markers onto an existing 'mpcross' object
Description
If the 'mpcross' object contains only genotypes and
pedigree, the markers are added to the genotypes after
some format checking. If the 'mpcross' object contains
estimated recombination fractions and LOD scores, the
markers are added in after estimating recombination
fractions with the existing markers. If the 'mpcross'
object contains a map, the markers are added onto the map
using 3-point mapping.
Usage
mpadd(mpcross1, mpcross2, r, theta = 0.15, LOD = 5, mapfx = c("haldane", "kosambi"))
Arguments
mpcross1
Original object of class mpcross
mpcross2
Additional object of class
mpcross
r
Grid of recombination fractions over which to
maximize likelihood
theta
Threshold for recombination fractions used
in constructing linkage groups
LOD
Threshold for LOD scores used in constructing
linkage groups
mapfx
Map function for converting recombination
distances to map distances
Value
Object of class 'mpcross' which is of the same stage as
the first object. Recombination fractions and linkage
groups will be recomputed after adding in the markers in
the second object if necessary.