debris_inc: gates out or assign indicators to debris particle.

In cyanoFilter: Cyanobacteria Population Identification for Flow Cytometry

Description

The function takes in a flowframe and identifies debris contained in the provided flowframe. It is specially designed for flowframe contaning both debris, BS4, BS5 and possibly other invading populations.

Usage

debris_inc(flowframe, p1, p2)

Arguments

flowframe	flowframe with debris and other cells.
p1	first flowcytometer channel that can be used to separate debris from the rest, e.g. "RED.B.HLin".
p2	second flowcytometer channel that can be used to separate debris from the rest, e.g. "YEL.B.HLin"

Details

The function uses the getPeaks and deGate functions in the flowDensity package to identify peaks between peaks 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.

Value

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

See Also

debris_nc

Examples

flowfile_path <- system.file("extdata", "text.fcs", package = "cyanoFilter",
              mustWork = TRUE)
flowfile <- flowCore::read.FCS(flowfile_path, alter.names = TRUE,
                               transformation = FALSE, emptyValue = FALSE,
                               dataset = 1) #FCS file contains only one data object
flowfile_nona <- cyanoFilter::nona(x = flowfile)
flowfile_noneg <- cyanoFilter::noneg(x = flowfile_nona)
flowfile_logtrans <- lnTrans(x = flowfile_noneg, c('SSC.W', 'TIME'))
cells_nonmargin <- cellmargin(flow.frame = flowfile_logtrans, Channel = 'SSC.W',
           type = 'estimate', y_toplot = "FSC.HLin")
debris_inc(flowframe = flowfile, p1 = "RED.B.HLin", p2 = "YEL.B.HLin")

cyanoFilter documentation built on Jan. 9, 2020, 5:08 p.m.