AggregateFlowFrames {FlowSOM} | R Documentation |
Aggregate multiple fcs files to analyze them simultaneously.
A new fcs file is written, which contains about cTotal
cells,
with ceiling(cTotal/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 (index plus or minus a
value between 0 and 0.1).
AggregateFlowFrames( fileNames, cTotal, channels = NULL, writeOutput = FALSE, outputFile = "aggregate.fcs", keepOrder = FALSE, silent = FALSE, ... )
fileNames |
Character vector containing full paths to the fcs files to aggregate |
cTotal |
Total number of cells to write to the output file |
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. |
silent |
If FALSE, prints an update every time it starts processing a new file. Default = FALSE. |
... |
Additional arguments to pass to read.FCS |
This function does not return anything, but will write a file with
about cTotal
cells to outputFile
# Define filename fileName <- system.file("extdata", "68983.fcs", package = "FlowSOM") # This example will sample 2 times 500 cells. ff_new <- AggregateFlowFrames(c(fileName, fileName), 1000)