extractClusters {CATALYST} | R Documentation |
daFrame
Extracts clusters from a daFrame
. Populations will be
either returned as a flowSet
or written to FCS files,
depending on argument as
.
extractClusters(x, k, ...) ## S4 method for signature 'daFrame' 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 |
... |
optional arguments. |
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 Lucia Crowell crowellh@student.ethz.ch
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")