clusterSamplesByComp {MineICA} | R Documentation

## Cluster samples from an IcaSet

### Description

This function allows to cluster samples according to the results of an ICA decomposition. One clustering is run independently for each component.

### Usage

      clusterSamplesByComp(icaSet, params,
        funClus = c("Mclust", "kmeans", "pam", "pamk", "hclust", "agnes"),
        filename, clusterOn = c("A", "S"),
        level = c("genes", "features"), nbClus,
        metric = "euclidean", method = "ward", ...)

### Arguments

`icaSet` | An `IcaSet` object
`params` | A `MineICAParams` object
`funClus` | The function to be used for clustering, must be one of `c("Mclust","kmeans","pam","pamk","hclust","agnes")`
`filename` | A file name to write the results of the clustering in
`clusterOn` | Specifies the matrix used to apply clustering: `"A"`: the clustering is performed in one dimension, on the vector of sample contributions, "S": the clustering is performed on the original data restricted to the contributing individuals.
`level` | The level of projections to be used when `clusterOn="S"`, either `"features"` or `"genes"`.
`nbClus` | The number of clusters to be computed, either a single number or a numeric vector whose length equals the number of components. If missing (only allowed if `funClus` is one of `c("Mclust","pamk")`)
`metric` | Metric used in `pam` and `hclust`, default is `"euclidean"`
`method` | Method of hierarchical clustering, used in `hclust` and `agnes`
`...` | Additional parameters required by the clustering function `funClus`.res <- clusterSamplesByComp(icaSet=icaSetCarbayo, params=params, funClus="kmeans",

### Value

A list consisting of three elements

clus:

  a list specifying the sample clustering for each component,

resClus:

  the complete output of the clustering function,

funClus:

  the function used to perform the clustering.

. When `clusterOn="S"`, if some components were not used because no contributing elements is selected using the cutoff, the icaSet with the corresponding component deleted is also returned.

### Author(s)

Anne Biton

### See Also

`Mclust`, `kmeans`, `pam`, `pamk`, `hclust`, `agnes`, `cutree`

### Examples

    data(icaSetCarbayo)
    params <- buildMineICAParams(resPath="carbayo/", selCutoff=4)

    ## cluster samples according to their contributions
    # using Mclust without a number of clusters
    res <- clusterSamplesByComp(icaSet=icaSetCarbayo, params=params, funClus="Mclust",
                                clusterOn="A", filename="clusA")

    # using kmeans
    res <- clusterSamplesByComp(icaSet=icaSetCarbayo, params=params, funClus="kmeans",
                                clusterOn="A", nbClus=2, filename="clusA")

[Package MineICA version 1.28.0 Index]