addloctocross {qtl} | R Documentation |
Add phenotype location into a cross object
Description
Add phenotype location(s) into a cross object (with eQTL/pQTL studies)
Usage
addloctocross(cross, locations=NULL, locfile="locations.txt", verbose=FALSE)
Arguments
cross |
An object of class |
locations |
R variable holding location information |
locfile |
load from a file, see the details section for the layout of the file. |
verbose |
If TRUE, give verbose output |
Details
inputfile layout: Num Name Chr cM 1 X3.Hydroxypropyl 4 50.0 Num is the number of the phenotype in the cross object Name is the name of the phenotype (will be checked against the name already in the cross object at position num Chr Chromosome cM position from start of chromosome in cM
Value
The input cross object, with the locations added as an additional component locations
Author(s)
Ritsert C Jansen; Danny Arends; Pjotr Prins; Karl W Broman broman@wisc.edu
See Also
-
mqmplot.cistrans
- Cis/trans plot 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
## Not run:
data(multitrait)
data(locations)
multiloc <- addloctocross(multitrait,locations)
results <- scanall(multiloc)
mqmplot.cistrans(results, multiloc, 5, FALSE, TRUE)
## End(Not run)