compensation of fcs file(s) from matrix

executes the classical compensation function on a flowSet or flowFrame, given a compensation matrix. The matrix can be either retrieved in the fcs files themselves or provided as a csv file.

Usage

compensateFromMatrix(
  x,
  matrixSource = c("fcs", "import"),
  matrixPath = NULL,
  updateChannelNames = TRUE,
  verbose = FALSE,
  ...
)

Arguments

x

a flowCore::flowFrame or flowCore::flowSet

matrixSource

if "fcs", the compensation matrix will be fetched from the fcs files (different compensation matrices can then be applied by fcs file) if "import", uses matrixPath to read the matrix (should be a csv file)

matrixPath

if matrixSource == "import", will be used as the input csv file path

updateChannelNames

if TRUE, updates the fluo channel names by prefixing them with "comp-"

verbose

if TRUE, displays information messages

...

additional arguments (not used)

Value

the compensated flowSet or flowFrame

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
fsRaw <- readSampleFiles(
    sampleFiles = sampleFiles,
    whichSamples = "all",
    truncate_max_range = truncateMaxRange,
    min.limit = minLimit)

suppressWarnings(ff_m <- removeMarginsPeacoQC(x = fsRaw[[2]]))
#> Removing margins from file : Donor2.fcs
    
ff_c <-
    compensateFromMatrix(ff_m,
                         matrixSource = "fcs")