cyto_load: Load .fcs files into ncdfFlowSet

In DillonHammill/CytoExploreR: Interactive Analysis of Cytometry Data

Description

cyto_load is a convenient wrapper around list.files and load_cytoset_from_fcs which makes it easy to load .fcs files into a cytoset. cyto_load is also a wrapper around load_gs to load saved GatingSet objects.

Usage

cyto_load(
  path = ".",
  select = NULL,
  exclude = NULL,
  sort = TRUE,
  barcode = FALSE,
  restrict = FALSE,
  ...
)

Arguments

path	points to the location of the .fcs files to read in. Preferably the name of folder in current working directory.
select	vector of file names to select when loading files, set to NULL be default to select all files in the specified directory.
exclude	vector of file names to exclude when loading files, set to NULL by default to load all files in the specified directory.
sort	logical indicating whether attempts should be made to sort the files by name prior to loading, set to TRUE by default.
barcode	logical indicating whether the flowFrames should be barcoded using cyto_barcode, set to FALSE by default.
restrict	logical indicating whether unassigned channels should be dropped from the returned cytoset, set to FALSE by default. See cyto_channels_restrict.
...	additional arguments passed to load_cytoset_from_fcs.

Value

object of class cytoset or GatingSet.

Author(s)

Dillon Hammill, [e-mail]

Examples

# Load in CytoExploreRData to access data
library(CytoExploreRData)

# Get path to Activation .fcs files in CytoExploreRData
datadir <- system.file("extdata", package = "CytoExploreRData")
path <- paste0(datadir, "/Activation")

# Load in .fcs files into cytoset
cs <- cyto_load(path)

# cs is a cytoset
class(cs)

DillonHammill/CytoExploreR documentation built on July 9, 2020, 1:53 a.m.