groupclusteredheatmap: Retrieving groups of traits after clustering

In kbroman/qtl: Tools for Analyzing QTL Experiments

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-off depends on the tree stucture and the amount of traits clustered using mqmplot.clusteredheatmap

Value

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

Author(s)

Danny Arends [e-mail]

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 <- fill.geno(multitrait) # impute missing genotype data
result <- mqmscanall(multitrait, logtransform=TRUE)
cresults <- mqmplot.clusteredheatmap(multitrait,result)
groupclusteredheatmap(multitrait,cresults,10)

kbroman/qtl documentation built on Jan. 13, 2024, 10:14 p.m.