Extract marker names

Source: R/cyto_channels-helpers.R

Extract marker names

# S3 method for GatingSet
cyto_markers(x, select = NULL, exclude = NULL, ...)

# S3 method for GatingHierarchy
cyto_markers(x, select = NULL, exclude = NULL, ...)

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

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

Arguments

x

object of class flowFrame, flowSet, GatingHierarchy or GatingSet.
select

vector of channels or markers for which the channel/marker combinations should be returned.
exclude

vector of channels or markers for which the channel/marker combinations should not be returned.
...

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 marker names or NULL if no markers have been assigned.

See also

cyto_channels

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_markers(fs[[1]])

#> Alexa Fluor 488-A              PE-A           7-AAD-A Alexa Fluor 405-A 
#>             "CD8"             "Va2"            "CD69"     "Hoechst-405" 
#> Alexa Fluor 430-A Alexa Fluor 647-A Alexa Fluor 700-A         APC-Cy7-A 
#>     "Hoechst-430"            "CD44"             "CD4"           "CD11c" 

# flowSet
cyto_markers(fs)

#> Alexa Fluor 488-A              PE-A           7-AAD-A Alexa Fluor 405-A 
#>             "CD8"             "Va2"            "CD69"     "Hoechst-405" 
#> Alexa Fluor 430-A Alexa Fluor 647-A Alexa Fluor 700-A         APC-Cy7-A 
#>     "Hoechst-430"            "CD44"             "CD4"           "CD11c" 

# GatingHierarchy
cyto_markers(gs[[1]])

#> Alexa Fluor 488-A              PE-A           7-AAD-A Alexa Fluor 405-A 
#>             "CD8"             "Va2"            "CD69"     "Hoechst-405" 
#> Alexa Fluor 430-A Alexa Fluor 647-A Alexa Fluor 700-A         APC-Cy7-A 
#>     "Hoechst-430"            "CD44"             "CD4"           "CD11c" 

# GatingSet
cyto_markers(gs)

#> Alexa Fluor 488-A              PE-A           7-AAD-A Alexa Fluor 405-A 
#>             "CD8"             "Va2"            "CD69"     "Hoechst-405" 
#> Alexa Fluor 430-A Alexa Fluor 647-A Alexa Fluor 700-A         APC-Cy7-A 
#>     "Hoechst-430"            "CD44"             "CD4"           "CD11c"