Restrict the channels of a cytometry object

Source: R/cyto_channels-helpers.R

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.

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

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

# S3 method for 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

Dillon Hammill, Dillon.Hammill@anu.edu.au

Examples


library(CytoExploreRData)

# Activation flowSet
fs <- Activation

# Channels
cyto_channels(fs)

#>  [1] "FSC-A"             "FSC-H"             "FSC-W"            
#>  [4] "SSC-A"             "SSC-H"             "SSC-W"            
#>  [7] "Alexa Fluor 488-A" "PE-A"              "PE-Texas Red-A"   
#> [10] "7-AAD-A"           "PE-Cy7-A"          "Alexa Fluor 405-A"
#> [13] "Alexa Fluor 430-A" "Qdot 605-A"        "Alexa Fluor 647-A"
#> [16] "Alexa Fluor 700-A" "APC-Cy7-A"         "Time"             

# Remove unused channels
fs <- cyto_channels_restrict(fs)

# Channels removed
cyto_channels(fs)

#>  [1] "FSC-A"             "FSC-H"             "FSC-W"            
#>  [4] "SSC-A"             "SSC-H"             "SSC-W"            
#>  [7] "Alexa Fluor 488-A" "PE-A"              "7-AAD-A"          
#> [10] "Alexa Fluor 405-A" "Alexa Fluor 430-A" "Alexa Fluor 647-A"
#> [13] "Alexa Fluor 700-A" "APC-Cy7-A"         "Time"