R/filterOut.R

In flowSpecs: Tools for processing of high-dimensional cytometry data

# Select events based on filter
#
#
# @param flowObj The fcs object to be subsetted. Both flowFrames and flowSets
# are accepted.
# @param filterName The name of the filter variable in the flow object to be
# used for the subsetting.
# @param withinFilter Should the events within or outsitde of the filter be
# selected?
# @return The flowObj, now smaller, as it only contains the data within,
# or outside of the filterName filter.
#' @importFrom flowCore fsApply
filterOut <- function(flowObj, filterName, withinFilter = TRUE) {
    if (withinFilter) {
        gateVal <- 1
    } else {
        gateVal <- 0
    }
    if (inherits(flowObj, "flowSet")) {
        resultObj <- fsApply(flowObj, function(x) {
            return(x[which(exprs(x[, filterName])[, 1] == gateVal), ])
        })
    } else if (inherits(flowObj, "flowFrame")) {
        resultObj <- flowObj[which(exprs(flowObj[, filterName])[, 1] ==
            gateVal), ]
    } else {
        stop("The flowObj needs to be either a flowSet or a flowFrame")
    }
    return(resultObj)
}