Generate overall marker expressions across Coereba clusters,

Usage

Coereba_MarkerExpressions(
  data,
  binary,
  panel,
  starter,
  returnType = "All",
  CombinatorialArgs = NULL
)

Arguments

data: The data.frame of clusters vs individual specimens, with the ratio values
binary: The data.frame of markers vs clusters, with 0 and 1 values
panel: A .csv or data.frame containing Fluorophore and Marker columns of your panel markers.
starter: A string containing the starting characters for all Coereba cluster names
returnType: Either "All" or "Combinatorial". Default is ALL.
CombinatorialArgs: When returnType Combinatorial, the two fluorophores to create quadrants for.

Value

returns a data.frame

Examples


File_Location <- system.file("extdata", package = "Coereba")
panelPath <- file.path(File_Location, "ILTPanelTetramer.csv")
panelData <- read.csv(panelPath, check.names=FALSE)
binaryPath <- file.path(File_Location, "HeatmapExample.csv")
binaryData <- read.csv(binaryPath, check.names=FALSE)
dataPath <- file.path(File_Location, "ReadyFileExample.csv")
dataData <- read.csv(dataPath, check.names=FALSE)

All <- Coereba_MarkerExpressions(data=dataData, binary=binaryData,
 panel=panelData, starter="SparkBlue550")

Memory <- Coereba_MarkerExpressions(data=dataData, binary=binaryData,
 panel=panelData, starter="SparkBlue550", returnType = "Combinatorial",
 CombinatorialArgs=c("BV510", "APC-Fire 750"))