cyto_channels_restrict: Restrict the channels of a cytometry object

In DillonHammill/CytoExploreR: Interactive Analysis of Cytometry Data

Restrict the channels of a cytometry object

Description

cyto_channels_restrict removes any unused channels (channels lacking marker assignments) from a flowFrame, flowSet, GatingHierarchy or GatingSet. By default, cyto_channels_restrict will always retain any FSC, SSC or Time channels irrespective of marker assignment. Removal of channels that contain marker assignments or channels that are privileged channels (FSC/SSC/Time) can be forced through use of the exclude argument.

Usage

## S3 method for class 'flowFrame'
cyto_channels_restrict(x, exclude = NULL, ...)

## S3 method for class 'flowSet'
cyto_channels_restrict(x, exclude = NULL, ...)

## S3 method for class 'GatingSet'
cyto_channels_restrict(x, exclude = NULL, ...)

Arguments

x	object of class flowFrame, flowSetor GatingSet.
exclude	vector of privileged channels or markers to remove in addition to the channels removed by default, set to NULL by default.
...	additional arguments passed to cyto_channels to control character matching for the exclude argument.

Value

an object of class flowFrame, flowSet, GatingHierarchy or GatingSet with unused channels removed.

Author(s)

Dillon Hammill, [e-mail]

Examples

library(CytoExploreRData)

# Activation flowSet
fs <- Activation

# Channels
cyto_channels(fs)

# Remove unused channels
fs <- cyto_channels_restrict(fs)

# Channels removed
cyto_channels(fs)

DillonHammill/CytoExploreR documentation built on March 2, 2023, 7:34 a.m.