Add phenotype location into a cross object
Add phenotype location(s) into a cross object (with eQTL/pQTL studies)
addloctocross(cross, locations=NULL, locfile="locations.txt", verbose=FALSE)
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 |
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
The input cross object, with the locations added as an additional component locations
Ritsert C Jansen; Danny Arends; Pjotr Prins; Karl W Broman broman@wisc.edu
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
## Not run:
data(multitrait)
data(locations)
multiloc <- addloctocross(multitrait,locations)
results <- scanall(multiloc)
mqmplot.cistrans(results, multiloc, 5, FALSE, TRUE)
## End(Not run)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.