flowDensity (version 1.6.0)

nmRemove: Preprocessing helper function for flow cytometry data

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=TRUE, talk=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

talk

if TRUE, it prints the margin event in each channel

Value

a 'FlowFrame' object.

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"),talk=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"))