Select samples based on experiment variables

Select samples based on experiment variables

cyto_select(x, ...)

Arguments

x	object of class flowSet or GatingSet.
...	named list containing experimental variables to be used to select samples or named arguments containing the levels of the variables to select. See below examples for use cases. Selected samples can be excluded by setting exclude to TRUE.

Value

flowSet or GatingSet restricted to samples which meet the designated selection criteria.

Author

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

Examples

# Load in CytoExploreRData to access data
library(CytoExploreRData)

# Look at experiment details
cyto_details(Activation)
#>                                name OVAConc Treatment
#> Activation_1.fcs   Activation_1.fcs       0    Stim-A
#> Activation_2.fcs   Activation_2.fcs       0    Stim-A
#> Activation_3.fcs   Activation_3.fcs       5    Stim-A
#> Activation_4.fcs   Activation_4.fcs       5    Stim-A
#> Activation_5.fcs   Activation_5.fcs      50    Stim-A
#> Activation_6.fcs   Activation_6.fcs      50    Stim-A
#> Activation_7.fcs   Activation_7.fcs     500    Stim-A
#> Activation_8.fcs   Activation_8.fcs     500    Stim-A
#> Activation_9.fcs   Activation_9.fcs       0    Stim-B
#> Activation_10.fcs Activation_10.fcs       0    Stim-B
#> Activation_11.fcs Activation_11.fcs       5    Stim-B
#> Activation_12.fcs Activation_12.fcs       5    Stim-B
#> Activation_13.fcs Activation_13.fcs      50    Stim-B
#> Activation_14.fcs Activation_14.fcs      50    Stim-B
#> Activation_15.fcs Activation_15.fcs     500    Stim-B
#> Activation_16.fcs Activation_16.fcs     500    Stim-B
#> Activation_17.fcs Activation_17.fcs       0    Stim-C
#> Activation_18.fcs Activation_18.fcs       0    Stim-C
#> Activation_19.fcs Activation_19.fcs       5    Stim-C
#> Activation_20.fcs Activation_20.fcs       5    Stim-C
#> Activation_21.fcs Activation_21.fcs      50    Stim-C
#> Activation_22.fcs Activation_22.fcs      50    Stim-C
#> Activation_23.fcs Activation_23.fcs     500    Stim-C
#> Activation_24.fcs Activation_24.fcs     500    Stim-C
#> Activation_25.fcs Activation_25.fcs       0    Stim-D
#> Activation_26.fcs Activation_26.fcs       0    Stim-D
#> Activation_27.fcs Activation_27.fcs       5    Stim-D
#> Activation_28.fcs Activation_28.fcs       5    Stim-D
#> Activation_29.fcs Activation_29.fcs      50    Stim-D
#> Activation_30.fcs Activation_30.fcs      50    Stim-D
#> Activation_31.fcs Activation_31.fcs     500    Stim-D
#> Activation_32.fcs Activation_32.fcs     500    Stim-D
#> Activation_33.fcs Activation_33.fcs       0        NA

# Select Stim-C samples with 0 and 500 nM OVA concentrations
fs <- cyto_select(Activation,
  Treatment = "Stim-C",
  OVAConc = c(0, 500)
)

# Select Stim-A and Stim-C treatment groups
fs <- cyto_select(
  Activation,
  list("Treatment" = c("Stim-A", "Stim-C"))
)

# Exclude Stim-D treatment group
fs <- cyto_select(Activation,
  Treatment = "Stim-D",
  exclude = TRUE
)