extractClusters {CATALYST} | R Documentation

## Extract clusters from a `daFrame`

### Description

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

### Usage

    extractClusters(x, k, ...)

    ## S4 method for signature 'daFrame,character'
    extractClusters(x, k, clusters = NULL,
      as = c("flowSet", "fcs"), out_dir = ".", verbose = TRUE)

### Arguments

`x` | a `daFrame`.
`k` | numeric or character string. Specifies the clustering to extract populations from. Must be one of `names(cluster_codes(x))`.
`...` | optional arguments.
`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 helena.crowell@uzh.ch

### Examples

    data(PBMC_fs, PBMC_panel, PBMC_md, merging_table)
    re <- daFrame(PBMC_fs, PBMC_panel, PBMC_md)

    # run clustering
    re <- cluster(re)

    # merge clusters
    re <- mergeClusters(re, k="meta20", table=merging_table, id="merging_1")
    extractClusters(re, k="merging_1")

[Package CATALYST version 1.8.7 Index]