mqmprocesspermutation: Convert mqmmulti objects into a scanoneperm object
In byandell/qtl: Tools for analyzing QTL experiments

Description Usage Arguments Value Author(s) See Also Examples

Function to convert mqmmulti objects into a scanoneperm object, this allows the use of R/qtl methods for permutation analysis that do not support the output of a multiple QTL scan using mqm's outputstructure.

1	mqmprocesspermutation(mqmpermutationresult = NULL)

mqmpermutationresult

mqmmulti object obtained after performing permutations on a single trait.using the function mqmpermutation

Output of the algorithm is a scanoneperm object. See also: summary.scanoneperm

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

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

f2qtl <- c(3,15,1,0)					# QTL at chromosome 3
data(map10)						# Mouse genetic map

f2cross <- sim.cross(map10,f2qtl,n=100,type="f2")	# Simulate a F2 Cross
## Not run: f2result <- mqmpermutation(f2cross,scanfunction=mqmscan)			# Bootstrap MQM mapping on the f2cross

f2perm <- mqmprocesspermutation(f2result)			# Create a permutation object
summary(f2perm)					# What LOD score is considered significant ?