Wrapper around flowCore::read.fcs() or flowCore::read.flowSet(). Also adds a "Cell_ID" additional column, used in flowFrames comparison
readSampleFiles(
sampleFiles,
whichSamples = "all",
nSamples = NULL,
seed = NULL,
pData = NULL,
channelMarkerFile = NULL,
...
)
a vector of character path to sample files
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
number of samples to randomly select
(if whichSamples == "random"
).
If nSamples
is higher than nb of available samples,
the output will be all samples
an optional seed parameters (provided to ease reproducibility).
an optional data.frame
containing
additional information for each sample file.
The pData
raw names must correspond to basename(sampleFiles)
.
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.
either a flowCore::flowSet or a flowCore::flowFrame if length(sampleFiles) == 1
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