notSubFrame: Removing a subset of a FlowFrame object

Description Usage Arguments Value Author(s) Examples

View source: R/flowDensity_methods.R

Description

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.

Usage

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

Arguments

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.

Value

a CellPopulation object.

Author(s)

Mehrnoush Malek <mmalekes@bccrc.ca>

Examples

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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"))

mehrnoushmalek/flowDensity documentation built on July 28, 2021, 12:10 p.m.