mqmfind.marker: Fetch significant markers after permutation analysis
In byandell/qtl: Tools for analyzing QTL experiments

Description Usage Arguments Value Author(s) See Also Examples

Fetch significant makers after permutation analysis. These markers can be used as cofactors for model selection in a forward stepwise approach.

1	mqmfind.marker(cross, mqmscan = NULL, perm = NULL, alpha = 0.05, verbose=FALSE)

`cross`	An object of class `cross`. See `read.cross` for details.
`mqmscan`	Results from either `scanone` or `mqmscan`
`perm`	a `scanoneperm` object
`alpha`	Threshold value, everything with significance < alpha is reported
`verbose`	Display more output on verbose=TRUE

returns a matrix with at each row a significant marker (determined from the scanoneperm object) and with columns: markername, chr and pos (cM)

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

mqmprocesspermutation - Function called to convert results from an mqmpermutation into an scanoneperm object
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

data(multitrait)				#Use the multitrait dataset
cof <- mqmsetcofactors(multitrait,3)		#Set cofactors at each 3th marker
multitrait <- fill.geno(multitrait)
multitrait <- transformPheno(multitrait, 7)     #log transform the 7th phenotype
## Not run: result <- mqmpermutation(multitrait,scanfunction=mqmscan,cofactors=cof,pheno.col=7,n.perm=50,batchsize=10)	# Bootstrap 50 runs in batches of 10

f2perm <- mqmprocesspermutation(result)		        #Create a permutation object
summary(f2perm)				        #What LOD score is considered significant ?
marker <- mqmfind.marker(multitrait,result[[1]],f2perm)		#Find markers with a significant QTL effect (First run is original phenotype data)
marker						#Print it to the screen