qtl (version 1.38-4)

groupclusteredheatmap: Retrieving groups of traits after clustering

Description

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

Usage

groupclusteredheatmap(cross, clusteredheatmapresult, 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-

Value

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

See Also

% \input{"inst/docs/Sources/MQM/mqm/standard_seealso.txt"}
• 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 % -----^^ inst/docs/Sources/MQM/mqm/standard_seealso.txt ^^-----

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)