R: Retrieving groups of traits after clustering

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 `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 danny.arends@gmail.com

### See Also

- 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

### 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)

[Package qtl version 1.41-6 Index]