View source: R/extractClusters.R
extractClusters | R Documentation |
SingleCellExperiment
Extracts clusters from a SingleCellExperiment
.
Populations will be either returned as a flowSet
or written to FCS files, depending on argument as
.
extractClusters(
x,
k,
clusters = NULL,
as = c("flowSet", "fcs"),
out_dir = ".",
verbose = TRUE
)
x |
a |
k |
numeric or character string.
Specifies the clustering to extract populations from.
Must be one of |
clusters |
a character vector.
Specifies which clusters to extract.
|
as |
|
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? |
a flowSet
or character vector of the output file names.
Mark D Robinson & Helena L Crowell helena.crowell@uzh.ch
# 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-"))
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