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'
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, Helena Lucia Crowell crowellh@student.ethz.ch

Examples

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")
[Package CATALYST version 1.4.2 Index]