debrisNc {cyanoFilter} | R Documentation |
The function takes in a flowframe and identifies debris contained in the provided flowframe.
debrisNc(flowframe, ch_chlorophyll, ch_p2, ph = 0.09, n_sd = 2)
flowframe |
flowframe with debris and other cells. |
ch_chlorophyll |
first flowcytometer channel that can be used to separate debris from the rest, e.g. "RED.B.HLin". |
ch_p2 |
second flowcytometer channel use for plotting from the rest, e.g. "YEL.B.HLin" |
ph |
the minimum peak height that should be considered. This aids the removal of tiny peaks. Defaults to 0.1 |
n_sd |
number of standard deviations away from peak should be considered to filter out debris |
The function uses the getPeaks
and
deGate
functions in the flowDensity
package to
identify peaks in ch_chlorophyll, and identify cut-off points
#between these peaks.
A plot of both channels supplied with horizontal line separating
debris from other cell populations is also returned.
list containing;
syn - flowframe containing non-debris particles
deb_pos - position of particles that are debris
syn_pos - position of particles that are not debris
flowfile_path <- system.file("extdata", "B4_18_1.fcs", package = "cyanoFilter", mustWork = TRUE) flowfile <- flowCore::read.FCS(flowfile_path, alter.names = TRUE, transformation = FALSE, emptyValue = FALSE, dataset = 1) flowfile_nona <- cyanoFilter::noNA(x = flowfile) flowfile_noneg <- cyanoFilter::noNeg(x = flowfile_nona) flowfile_logtrans <- cyanoFilter::lnTrans(x = flowfile_noneg, c('SSC.W', 'TIME')) cells_nonmargin <- cellMargin(flowframe = flowfile_logtrans, Channel = 'SSC.W', type = 'estimate', y_toplot = "FSC.HLin") debrisNc(flowframe = reducedFlowframe(cells_nonmargin), ch_chlorophyll = "RED.B.HLin", ch_p2 = "YEL.B.HLin", ph = 0.05)