mqmsetcofactors {qtl} | R Documentation |
Set cofactors at fixed intervals, to be used with MQM
Description
Set cofactors, at fixed marker intervals. Together
with mqmscan
cofactors are selected through backward elimination.
Usage
mqmsetcofactors(cross, each = NULL, cofactors=NULL, sexfactors=NULL, verbose=FALSE)
Arguments
cross |
An object of class |
each |
Every 'each' marker will be used as a cofactor, when each is used the |
cofactors |
List of cofactors to be analysed in the QTL model. To set cofactors use |
sexfactors |
list of markers which should be treated as dominant cofactors (sexfactors), when |
verbose |
If TRUE, print tracing information. |
Value
An list of cofactors to be passed into mqmscan
.
Author(s)
Ritsert C Jansen; Danny Arends; Pjotr Prins; Karl W Broman broman@wisc.edu
See Also
The MQM tutorial: https://rqtl.org/tutorials/MQM-tour.pdf
-
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
Examples
data(hyper) # Hyper dataset
hyperfilled <- fill.geno(hyper)
# Automatic cofactors every third marker
cofactors <- mqmsetcofactors(hyperfilled,3)
result <- mqmscan(hyperfilled,cofactors) # Backward model selection
mqmgetmodel(result)
#Manual cofactors at markers 3,6,9,12,40 and 60
cofactors <- mqmsetcofactors(hyperfilled,cofactors=c(3,6,9,12,40,60))
result <- mqmscan(hyperfilled,cofactors) # Backward model selection
mqmgetmodel(result)