Extract channel names

Simply a wrapper around colnames to extract the channels associated with a flowFrame, flowSet or GatingSet.

cyto_channels(x, select = NULL, exclude = NULL, ...)

Arguments

x	object of class flowFrame, flowSet, GatingHierarchy or GatingSet.
select	vector of channel names to select.
exclude	vector of channel names to exclude.
...	additional arguments passed to grepl for character matching. For exact character string matching to override the default which ignores character case, set fixed to TRUE.

Value

vector of channel names.

See also

cyto_fluor_channels

Author

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

Examples

# Load in CytoExploreRData to access data
library(CytoExploreRData)

# Activation flowSet
fs <- Activation

# Activation GatingSet
gs <- GatingSet(fs)

# flowFrame
cyto_channels(fs[[1]])
#>  [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"             

# flowSet
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"             

# GatingHierarchy
cyto_channels(gs[[1]])
#>  [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"             

# GatingSet - exclude FSC & SSC channels
cyto_channels(gs, exclude = c("FSC","SSC"))
#>  [1] "Alexa Fluor 488-A" "PE-A"              "PE-Texas Red-A"   
#>  [4] "7-AAD-A"           "PE-Cy7-A"          "Alexa Fluor 405-A"
#>  [7] "Alexa Fluor 430-A" "Qdot 605-A"        "Alexa Fluor 647-A"
#> [10] "Alexa Fluor 700-A" "APC-Cy7-A"         "Time"