nmRemove: Preprocessing helper function for flow cytometry data

Description Usage Arguments Value Author(s) Examples

View source: R/flowDensity_methods.R

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

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	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 <[email protected]> Mehrnoush Malek <[email protected]>

Examples

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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"))

mehrnoushmalek/flowDensity documentation built on Oct. 26, 2019, 2:26 p.m.