subset: Functions to subset ClusterExperiment Objects
In clusterExperiment: Compare Clusterings for Single-Cell Sequencing

Description Usage Arguments Details Value Examples

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

## 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")
)

`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"`)

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.

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

#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")