Aggregate and sample multiple flow frames of a flow set together

Aggregate multiple flow frames in order to analyze them simultaneously. A new FF, which contains about nTotalEvents cells, nTotalEvents/nFiles cells from each file. Two new columns are added: a column indicating the original file by index, and a noisy version of this, for better plotting opportunities, This function is based on PeacoQC::AggregateFlowframes() where file names inputs have been replaced by a flowSet input.

Usage

aggregateAndSample(
  fs,
  nTotalEvents,
  setup = c("forceNEvent", "forceBalance"),
  seed = NULL,
  channels = NULL,
  writeOutput = FALSE,
  outputFile = "aggregate.fcs",
  keepOrder = FALSE
)

Arguments

fs

a flowCore::flowset

nTotalEvents

Total number of cells to select from the input flow frames

setup

How to proceed when nTotalEvents/nFiles is too high for some of the flow frames:

forceBalance (default): compute the minimum nb of events per flow frame, and keep that amount of events from each flow frame.
forceNEvents: try to be as balanced as possible, but force a total of nTotalEvents if possible, i.e. takes all events from the flow frame with too low nb of events, and then fill in the total with events from the bigger flow frames in a balanced way. However, if nTotalEvents is greater than the sum of all events, take all events only once.

seed

seed to be set before sampling for reproducibility. Default NULL does not set any seed.

channels

Channels/markers to keep in the aggregate. Default NULL takes all channels of the first file.

writeOutput

Whether to write the resulting flowframe to a file. Default FALSE

outputFile

Full path to output file. Default "aggregate.fcs"

keepOrder

If TRUE, the random subsample will be ordered in the same way as they were originally ordered in the file. Default = FALSE.

Value

returns a new flowCore::flowFrame

Examples


data(OMIP021Samples)

nCells <- 1000
agg <- aggregateAndSample(
    fs = OMIP021Samples,
    nTotalEvents = nCells)