extractClusters: Extract clusters from a 'SingleCellExperiment'

In CATALYST: Cytometry dATa anALYSis Tools

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 & Helena L Crowell [e-mail]

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-"))

CATALYST documentation built on Nov. 8, 2020, 6:53 p.m.