| groupclusteredheatmap {qtl} | R Documentation |
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 |
clusteredheatmapresult |
Resultint dendrogram object from |
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 |
Value
A list containing groups of traits which were clustered together with a distance less that height
Author(s)
Danny Arends danny.arends@gmail.com
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)