extractClusters {CATALYST} | R Documentation

## Extract clusters from a `SingleCellExperiment`

### Description

Extracts clusters from a `SingleCellExperiment`. Populations will be either returned as a `flowSet` or written to FCS files, depending on argument `as`.

### Usage

    extractClusters(
      x,
      k,
      clusters = NULL,
      as = c("flowSet", "fcs"),
      out_dir = ".",
      verbose = TRUE
    )

### Arguments

`x` | a `SingleCellExperiment`.
`k` | numeric or character string. Specifies the clustering to extract populations from. Must be one of `names(cluster_codes(x))`.
`clusters` | a character vector. Specifies which clusters to extract. `NULL` = all clusters.
`as` | `"flowSet"` or `"fcs"`. Specifies whether clusters should be return as a `flowSet` or written to FCS files.
`out_dir` | a character string. Specifies where FCS files should be writen to. Defaults to the working directory.
`verbose` | logical. Should information on progress be reported?

### Value

a `flowSet` or character vector of the output file names.

### Author(s)

Mark D Robinson and Helena Lucia Crowell

### Examples

    # construct SCE & run clustering
    data(PBMC_fs, PBMC_panel, PBMC_md, merging_table)
    sce <- prepData(PBMC_fs, PBMC_panel, PBMC_md)
    sce <- cluster(sce)

    # merge clusters
    sce <- mergeClusters(sce, k="meta20", table=merging_table, id="merging_1")
    extractClusters(sce, k="merging_1", clusters=c("NK cells", "surface-"))

[Package CATALYST version 1.10.3 Index]