R/flowdex.R

In bpollner/flowdex: Extract Fluorescence Distribution Data from FCS Files and Recalculate to Events per Volume

#' @title Extract Fluorescence Distribution Data from FCS Files and Recalculate
#' to Events per Volume
#' @description Extract fluorescence distribution data from any bivariate
#' distribution within a previously defined flow cytometry gating set and
#' recalculate the fluorescence distribution data to events per volume.
#' To (meaningfully) use flowdex, the FCM files have to contain volumetric
#' measurement data denoting the acquired sample volume.
#' @details When calling \code{\link{flowdexit}}, the gating set "gs" is
#' assigned to the parent envelope.
#' @section Important: In order to be able to correctly re-calculate raw events
#' to events per volume unit, it is paramount to obtain the correct volume
#' factor from the manual of the FCM-machine / the volumetric measurement
#' module. Please see the section 'Calculating Events per Volume Unit'
#' at \code{\link{flowdexit}} for further details.
#' @section CAVE: Some functions like e.g. \code{\link{repairVolumes}},
#' \code{\link{repairSID}} or \code{\link{checkRepairFcsFiles}} can re-write
#' fcs files to disc, thereby overwriting original fcs files. It is therefore
#' recommended to work on a copy of the original fcs files.
#' @author Bernhard Pollner
#' @section Maintainer: Bernhard Pollner <bernhard.pollner@@mac.com>
#' @section Links: Please see \url{https://bpollner.github.io/flowdex/} for
#' practical examples and a small tutorial; bug reports can be made at
#' \url{https://github.com/bpollner/flowdex/issues}.
#' @section Important functions: \code{\link{flowdexit}}
#' @section Acknowledgements: This work was made possible by support from IPF
#' Austria - Georg Huber. \cr
#' Flow cytometry data were acquired at the Institute
#' for Hygiene and Medical Microbiology, Medical University of Innsbruck,
#' Austria.
#' @import methods
#' @import utils
#'
#' @importClassesFrom flowWorkspace GatingSet
#'
#' @importFrom graphics abline lines axis legend matplot
#' @importFrom grDevices dev.off pdf colorRampPalette rgb
#'
#' @docType package
#' @name flowdex
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