findCluster {GLAD} | R Documentation

## Clustering of genomic regions

### Description

The function `findCluster` allows the clustering of regions.

### Usage

    findCluster.profileChr(profileChr, region="Region", genome=TRUE,
                           lambda=10, nmin=1, nmax=10, type="tricubic",
                           param=c(d=6), verbose=FALSE, ...)

### Arguments

`profileChr` | Object of class `profileChr`.
`region` | Label which indicated where outliers are detected.
`genome` | If `TRUE`, the "MSHR clustering by chromosome" clustering step is run otherwise it is the "HCSR clustering throughout the genome" clustering step.
`lambda` | Penalty λ*.
`nmin` | Minimal number of cluster to find.
`nmax` | Maximal number of cluster to find.
`type` | Type of kernel to use in the penalty term (this arguments is passed to the `kernelpen` function).
`param` | Parameters of the kernel (this arguments is passed to the `kernelpen` function).
`verbose` | If `TRUE` some information are printed
`...` | Risk alpha used in `detectOutliers`.

### Value

An object of class `profileChr` with the following element added to the data.frame `profileValues`:
either:

`ZoneChr` | indicates the regions which belongs to the same HCSR (if `genome=FALSE`).
`ZoneGen` | indicates HCSR which belongs to the same cluster (if `genome=TRUE`).

### Author(s)

Philippe Hupé, Philippe.Hupe@curie.fr.

### See Also

`glad`, `detectOutliers`

[Package GLAD version 1.0.1 Index]