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'
    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, Helena Lucia Crowell crowellh@student.ethz.ch

### Examples

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

    # run clustering
    lineage <- c("CD3", "CD45", "CD4", "CD20", "CD33",
        "CD123", "CD14", "IgM", "HLA_DR", "CD7")
    re <- cluster(re, cols_to_use=lineage)

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

[Package CATALYST version 1.4.2 Index]