nmRemove: Preprocessing helper function for flow cytometry data

In RGLab/flowDensity: Sequential Flow Cytometry Data Gating

Description

Remove the margin events on the axes. Usually, these events are considered as debris or artifacts. This is specifically useful for 'FSC' and 'SSC' channels in a 'FlowFrame' object. However, any channel can be input as an argument.

Usage

	nmRemove(  flow.frame, channels, neg=FALSE, verbose=FALSE,return.ind=FALSE)

Arguments

flow.frame	a 'FlowFrame' object.
channels	a vector of channel names or their corresponding indices.
neg	if TRUE, negative events are also removed
verbose	if TRUE, it prints the margin event in each channel
return.ind	if TRUE, it return indices of margin events for each channel.

Value

a 'FlowFrame' object, or a 'list' of indices identifying margin events for each channel.

Author(s)

Jafar Taghiyar <[e-mail]> Mehrnoush Malek <[e-mail]>

Examples

data_dir <- system.file("extdata", package = "flowDensity")
load(list.files(pattern = 'sampleFCS_2', data_dir, full = TRUE))
#Removing margin events of FSC-A and SSC-A channels
no.margin <- nmRemove(f2, c("FSC-A","SSC-A"),verbose=TRUE)
plotDens(f2, c("FSC-A","SSC-A"))
# Scatter plot of FSC-A vs. SSC-A after removing margins
plotDens(no.margin, c("FSC-A","SSC-A"))

RGLab/flowDensity documentation built on Sept. 12, 2019, 6:47 a.m.