Generate overall marker expressions across Coereba clusters,

Usage

Coereba_MarkerExpressions2(
  x,
  theassay = "ratios",
  returnType = "All",
  CombinatorialArgs = NULL
)

Arguments

x: The Coereba Summarized Experiment object from Coereba_Processing
returnType: Either "All" or "Combinatorial". Default is ALL.
CombinatorialArgs: When returnType Combinatorial, the two fluorophores to create quadrants for.
TheAssay: Default is "ratios"

Value

returns a data.frame

Examples


File_Location <- system.file("extdata", package = "Coereba")
panelPath <- file.path(File_Location, "ILTPanelTetramer.csv")

files <- gs_pop_get_data(gs, "CD4")
#> Error: object 'gs' not found
MySE <- Coereba_Processing(x=files[[1]], panel=panelPath)
#> Error: object 'files' not found

All <- Coereba_MarkerExpressions2(x=MySE)
#> Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'metadata': object 'MySE' not found

Memory <- Coereba_MarkerExpressions2(x=MySE, returnType = "Combinatorial",
 CombinatorialArgs=c("BV510", "APC-Fire 750"))
#> Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'metadata': object 'MySE' not found