addloctocross: Add phenotype location into a cross object
In byandell/qtl: Tools for analyzing QTL experiments

Description Usage Arguments Details Value Author(s) See Also Examples

Add phenotype location(s) into a cross object (with eQTL/pQTL studies)

1	addloctocross(cross, locations=NULL, locfile="locations.txt", verbose=FALSE)

`cross`	An object of class `cross`. See `read.cross` for details.
`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 postion from start of chromosome in cM

The input cross object, with the locations added as an aditional component locations

Ritsert C Jansen; Danny Arends; Pjotr Prins; Karl W Broman kbroman@biostat.wisc.edu

mqmplot.cistrans - Cis/trans plot
The MQM tutorial: http://www.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)