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,character'
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 and Helena Lucia Crowell helena.crowell@uzh.ch

Examples

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

# run clustering
re <- cluster(re)

# merge clusters
re <- mergeClusters(re, k="meta20", table=merging_table, id="merging_1")
extractClusters(re, k="merging_1")


[Package CATALYST version 1.8.3 Index]