Read fcs sample files — readSampleFiles • CytoPipeline

Wrapper around flowCore::read.fcs() or flowCore::read.flowSet(). Also adds a "Cell_ID" additional column, used in flowFrames comparison

Usage

readSampleFiles(
  sampleFiles,
  whichSamples = "all",
  nSamples = NULL,
  seed = NULL,
  channelMarkerFile = NULL,
  ...
)

Arguments

sampleFiles

a vector of character path to sample files

whichSamples

one of:

'all' if all sample files need to be read
'random' if some samples need to be chosen randomly (in that case, using nSamples and seed)
a vector of indexes pointing to the sampleFiles vector

nSamples

number of samples to randomly select (if whichSamples == "random"). If nSamples is higher than nb of available samples, the output will be all samples

seed

an optional seed parameters (provided to ease reproducibility).

channelMarkerFile

an optional path to a csv file which provides the mapping between channels and markers. If provided, this csv file should contain a Channel column, and a Marker column. Optionally a 'Used' column can be provided as well (TRUE/FALSE). Channels for which the 'Used' column is set to FALSE will not be incorporated in the created flowFrame.

...

additional parameters passed to flowCore file reading functions.

Value

either a flowCore::flowSet or a flowCore::flowFrame if length(sampleFiles) == 1

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)

#res

# create a flowCore::flowFrame with one single sample
res2 <- readSampleFiles(
    sampleFiles = sampleFiles,
    whichSamples = 2,
    truncate_max_range = truncateMaxRange,
    min.limit = minLimit)

#res2