subset {clusterExperiment} | R Documentation

## Functions to subset ClusterExperiment Objects

### Description

These functions are used to subset ClusterExperiment objects, either by removing samples, genes, or clusterings

### Usage

    ## S4 method for signature 'ClusterExperiment'
    removeClusterings(x, whichClusters)

    ## S4 method for signature 'ClusterExperiment'
    removeClusters(
      x,
      whichCluster,
      clustersToRemove,
      makePrimary = FALSE,
      clusterLabels = NULL
    )

    ## S4 method for signature 'ClusterExperiment,ANY,character,ANY'
    x[i, j, ..., drop = TRUE]

    ## S4 method for signature 'ClusterExperiment,ANY,logical,ANY'
    x[i, j, ..., drop = TRUE]

    ## S4 method for signature 'ClusterExperiment,ANY,numeric,ANY'
    x[i, j, ..., drop = TRUE]

    ## S4 method for signature 'ClusterExperiment'
    subsetByCluster(
      x,
      clusterValue,
      whichCluster = "primary",
      matchTo = c("name", "clusterIds")
    )

### Arguments

`x` | a ClusterExperiment object.
`whichClusters` | argument that can be either numeric or character vector indicating the clusterings to be used. See details of `getClusterIndex`.
`whichCluster` | argument that can be a single numeric or character value indicating the single clustering to be used. Giving values that result in more than one clustering will result in an error. See details of `getClusterIndex`.
`clustersToRemove` | numeric vector identifying the clusters to remove (whose samples will be reassigned to -1 value).
`makePrimary` | whether to make the added cluster the primary cluster (only relevant if `y` is a vector)
`clusterLabels` | label(s) for the clusters being added. If `y` a matrix, the column names of that matrix will be used by default, if `clusterLabels` is not given.
`i, j` | A vector of logical or integer subscripts, indicating the rows and columns to be subsetted for `i` and `j`, respectively.
`...` | The arguments `transformation`, `clusterTypes` and `clusterInfo` to be passed to the constructor for signature `SingleCellExperiment,matrix`.
`drop` | A logical scalar that is ignored.
`clusterValue` | values of the cluster to match to for subsetting
`matchTo` | whether to match to the cluster name (`"name"`) or internal cluster id (`"clusterIds"`)

### Details

`removeClusterings` removes the clusters given by `whichClusters`. If the `primaryCluster` is one of the clusters removed, the `primaryClusterIndex` is set to 1 and the dendrogram and coclustering matrix are discarded and orderSamples is set to `1:NCOL(x)`.

`removeClusters` creates a new cluster that unassigns samples in cluster `clustersToRemove` (in the clustering defined by `whichClusters`) and assigns them to -1 (unassigned)

Note that when subsetting the data, the dendrogram information and the co-clustering matrix are lost.

### Value

A `ClusterExperiment` object.

`removeClusterings` returns a `ClusterExperiment` object, unless all clusters are removed, in which case it returns a `SingleCellExperiment` object.

`subsetByCluster` subsets the object by clusters in a clustering and returns a ClusterExperiment object with only those samples

### Examples

    #load CE object
    data(rsecFluidigm)
    # remove the mergeClusters step from the object
    clusterLabels(rsecFluidigm)
    test<-removeClusterings(rsecFluidigm,whichClusters="mergeClusters")
    clusterLabels(test)
    tableClusters(rsecFluidigm)
    test<-removeClusters(rsecFluidigm,whichCluster="mergeClusters",clustersToRemove=c("m01","m04"))
    tableClusters(test,whichCluster="mergeClusters")

[Package clusterExperiment version 2.12.0 Index]