mqmautocofactors {qtl} | R Documentation |
Sets cofactors, taking underlying marker density into account. Together
with mqmscan
cofactors are selected through backward elimination.
mqmautocofactors(cross, num=50, distance=5, dominance=FALSE, plot=FALSE, verbose=FALSE)
cross |
An object of class cross . See read.cross for details.
|
num |
Number of cofactors to set (warns when setting too many cofactors). |
distance |
Minimal distance between two cofactors, in cM. |
dominance |
If TRUE, create a cofactor list that is safe to use
with the dominance scan mode of MQM. See mqmscan for details. |
plot |
If TRUE, plots a genetic map displaying the selected markers as cofactors. |
verbose |
If TRUE, give verbose output. |
A list of cofactors to be used with mqmscan
.
Ritsert C Jansen; Danny Arends; Pjotr Prins; Karl W Broman kbroman@biostat.wisc.edu
MQM
- MQM description and references
mqmscan
- Main MQM single trait analysis
mqmscanall
- Parallellized traits analysis
mqmaugment
- Augmentation routine for estimating missing data
mqmautocofactors
- Set cofactors using marker density
mqmsetcofactors
- Set cofactors at fixed locations
mqmpermutation
- Estimate significance levels
scanone
- Single QTL scanning
data(hyper) # hyper dataset hyperfilled <- fill.geno(hyper) cofactors <- mqmautocofactors(hyperfilled,15) # Set 15 Cofactors result <- mqmscan(hyperfilled,cofactors) # Backward model selection mqmgetmodel(result)