extractClusters {CATALYST} | 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 |
|
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 and Helena Lucia Crowell
# 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-"))