notSubFrame: Removing a subset of a FlowFrame object
In flowDensity: Sequential Flow Cytometry Data Gating

Description Usage Arguments Value Author(s) Examples

View source: R/flowDensity_methods.R

Remove a subset of a FlowFrame object specified by gates from the flowDensity method. It comes in handy when one needs the complement of a cell population in the input flow cytometry data.

1	notSubFrame(obj, channels, position = NA, gates, filter)

`obj`	a 'FlowFrame' or 'cellPopulation' object.
`channels`	a vector of two channel names or their corresponding indices in the 'flow.frame'.
`position`	a vector of two logical values specifying the position of the cell subset of interest on the 2D plot.
`gates`	the gates slot in the CellPoulation object which is output by flowDensity function. It can also be a vector of two integer values each of which specifies a threshold for the corresponding channel in 'channels' argument.
`filter`	boundary of the subset to be removed. This value is stored in the 'filter' slot of a 'CellPopulation' object.

a CellPopulation object.

Mehrnoush Malek <mmalekes@bccrc.ca>

data_dir <- system.file("extdata", package = "flowDensity")
load(list.files(pattern = 'sampleFCS_1', data_dir, full = TRUE))
#Find the threshold for CD20
cd20.gate <- deGate(f,channel="APC-H7-A")
# Gate out the CD20- populations using the notSubFrame
CD20.pos <- notSubFrame(f,channels=c("APC-H7-A","PerCP-Cy5-5-A"),position=c(FALSE,NA),gates=c(cd20.gate,NA))
#Plot the CD20+ cells on same channels
plotDens(CD20.pos@flow.frame,c("APC-H7-A","PerCP-Cy5-5-A"))