qtl (version 1.66)

groupclusteredheatmap: Retrieving groups of traits after clustering

Description

Retrieving groups of clustered traits from the output of mqmplot.clusteredheatmap.

Usage

groupclusteredheatmap(cross, clusteredheatmapresult, height)

Value

A list containing groups of traits which were clustered together with a distance less that height

Arguments

cross

An object of class cross. See read.cross for details.

clusteredheatmapresult

Resultint dendrogram object from mqmplot.clusteredheatmap

height

Height at which to 'cut' the dendrogram, a higher cut-off gives less but larger groups. Height represents the maximum distance between two traits clustered together using hclust. the 'normal' behaviour of bigger groups when using a higher heigh cut-off depends on the tree stucture and the amount of traits clustered using mqmplot.clusteredheatmap

Author

Danny Arends

See Also

• 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

data(multitrait)
multitrait <- subset(multitrait, chr=1:2, ind=!apply(multitrait$pheno, 1, function(a) any(is.na(a))))
multitrait$pheno <- multitrait$pheno[,1:3]
multitrait <- fill.geno(multitrait) # impute missing genotype data
result <- mqmscanall(multitrait, logtransform=TRUE)
cresults <- mqmplot.clusteredheatmap(multitrait,result)
groupclusteredheatmap(multitrait,cresults,10)