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write flowFrame to disk

Source: R/utils.R
writeFlowFrame.Rd

wrapper around flowCore::write.FCS() or utils::write.csv that discards any additional parameter passed in (...)

Usage

writeFlowFrame(
  ff,
  dir = ".",
  useFCSFileName = TRUE,
  prefix = "",
  suffix = "",
  format = c("fcs", "csv"),
  csvUseChannelMarker = TRUE,
  ...
)

Arguments

ff

a flowCore::flowFrame

dir

an existing directory to store the flowFrame,

useFCSFileName

if TRUE filename used will be based on original fcs filename

prefix

file name prefix

suffix

file name suffix

format

either fcs or csv

csvUseChannelMarker

if TRUE (default), converts the channels to the corresponding marker names (where the Marker is not NA). This setting is only applicable to export in csv format.

...

other arguments (not used)

Value

nothing

Examples

rawDataDir <-
    system.file("extdata", package = "CytoPipeline")
sampleFiles <-
    file.path(rawDataDir, list.files(rawDataDir, pattern = "Donor"))

truncateMaxRange <- FALSE
minLimit <- NULL

# create flowCore::flowSet with all samples of a dataset
res <- readSampleFiles(
    sampleFiles = sampleFiles,
    whichSamples = "all",
    truncate_max_range = truncateMaxRange,
    min.limit = minLimit)
    
ff_c <- compensateFromMatrix(res[[2]], matrixSource = "fcs") 
outputDir <- base::tempdir()
writeFlowFrame(ff_c, 
               dir = outputDir,
               suffix = "_fcs_export",
               format = "csv")