nmRemove {flowDensity} | R Documentation

## 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=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 <jtaghiyar@bccrc.ca> Mehrnoush Malek <mmalekes@bccrc.ca>

### 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"))

[Package flowDensity version 1.20.0 Index]