Main Luciernaga Function, normalized on individual cell level

Usage

Luciernaga_QC(
  x,
  subsets,
  sample.name,
  removestrings = NULL,
  Verbose = FALSE,
  experiment = NULL,
  experiment.name = NULL,
  condition = NULL,
  condition.name = NULL,
  AFOverlap,
  unmixingcontroltype = "both",
  Unstained = FALSE,
  ratiopopcutoff = 0.01,
  stats = "median",
  Subtraction = "Internal",
  desiredAF = NULL,
  BeadAF = NULL,
  BeadMainAF = NULL,
  CellAF = NULL,
  CellMainAF = NULL,
  SignatureReturnNow = FALSE,
  Increments,
  LocalMaximaRatio = 0.15,
  SecondaryPeaks = 2,
  RetainedType = "normalized",
  Brightness = FALSE,
  ExportType,
  minimalfcscutoff = 0.05,
  SCData = "subtracted",
  NegativeType = "default",
  TotalNegatives = 500,
  outpath
)

Arguments

x: A Gating Set object (ex. gs or gs[[1]])
subsets: The Gating Hierarchy level you will be sampling at
sample.name: Keyword variable which samples are stored (ex. "GUID")
removestrings: A string of character values to remove from sample.name
Verbose: Whether to print outputs as you go.
experiment: Provide directly experiment name (ex. "JAN2024")
experiment.name: Keyword variable which experiment information is stored (ex. "TUBENAME")
condition: Provide directly experiment name (ex. "JAN2024")
condition.name: Keyword variable which experiment information is stored (ex. "TUBENAME")
AFOverlap: A data.frame or a filepath to the CSV containing the Autofluorescence overlap of individual fluorophores for exclusion
unmixingcontroltype: Whether your inputs are "cells", "beads" or "both"
Unstained: Set to True when running unstained samples that don't have Unstained in the Name
ratiopopcutoff: A numeric ratio for peak detector inclusion, default is set to 0.01 all startingcells
stats: Whether to take "mean" or "median"
Subtraction: Whether for single color controls to use "Internal", "Internal_General" or "External" autofluorescence
desiredAF: Main Autofluorescence Detector (ex. "V7-A")
BeadAF: A passed data.frame row containing the reference for bead unstained.
BeadMainAF: The detector that corresponds to the "main" bead AF, albeit dim.
CellAF: A passed data.frame row containing the reference for cell unstained.
CellMainAF: The detector that corresponds to the "main" cell AF.
SignatureReturnNow: Short circuits the function and returns signature for specified autofluorescence.
Increments: Rounding parameter, default is set to 0.1
LocalMaximaRatio: Height of peaks to proceed
SecondaryPeaks: Number of Secondary Peaks, default is set to 2.
RetainedType: Whether to return "raw" or "normalized" values for lineplots.
Brightness: Whether sum of detectors should be returned.
ExportType: Whether to return "fcs", "data"
minimalfcscutoff: A ratio determining number cells needed for .fcs export
SCData: Whether to return "subtracted" or "raw" data for single colors
NegativeType: Whether to append a negative pop to .fcs file, "default", "artifical" or "samples"
TotalNegatives: When setting NegativeType to "artificial" or "sample", how many events to add.
outpath: Location where created .fcs and .csv files are sent

Value

Additional information to be added

Examples


library(flowCore)
library(flowWorkspace)
library(openCyto)
library(data.table)
library(dplyr)
library(purrr)
library(stringr)

File_Location <- system.file("extdata", package = "Luciernaga")
FCS_Files <- list.files(path = File_Location, pattern = ".fcs",
  full.names = TRUE)
CellSingleColorFiles <- FCS_Files[grep("Cells", FCS_Files)]
CellSingleColors <- CellSingleColorFiles[!str_detect("Unstained", CellSingleColorFiles)]
MyCytoSet <- load_cytoset_from_fcs(CellSingleColors[1:2],
  truncate_max_range = FALSE,transformation = FALSE)
MyGatingSet <- GatingSet(MyCytoSet)
MyGates <- fread(file.path(path = File_Location, pattern = 'Gates.csv'))
MyGatingTemplate <- gatingTemplate(MyGates)
#> Adding population:singletsFSC
#> Adding population:singletsSSC
#> Adding population:singletsSSCB
#> Adding population:nonDebris
#> Adding population:lymphocytes
gt_gating(MyGatingTemplate, MyGatingSet)
#> Gating for 'singletsFSC'
#> done!
#> done.
#> Gating for 'singletsSSC'
#> done!
#> done.
#> Gating for 'singletsSSCB'
#> done!
#> done.
#> Gating for 'nonDebris'
#> done!
#> done.
#> Gating for 'lymphocytes'
#> The prior specification has no effect when usePrior=no
#> Using the serial version of flowClust
#> The prior specification has no effect when usePrior=no
#> Using the serial version of flowClust
#> done!
#> done.
#> finished.
removestrings <-  c("DR_", "Cells", ".fcs", "-", " ")
StorageLocation <- file.path("C:", "Users", "JohnDoe", "Desktop")

FileLocation <- system.file("extdata", package = "Luciernaga")
pattern = "AutofluorescentOverlaps.csv"
AFOverlap <- list.files(path=FileLocation, pattern=pattern, full.names = TRUE)

SingleColor_Data <- map(.x=MyGatingSet[1:2], .f=Luciernaga_QC, subsets="lymphocytes",
 removestrings=removestrings, sample.name="GUID", unmixingcontroltype = "cells",
 Unstained = FALSE, ratiopopcutoff = 0.001, Verbose = FALSE, AFOverlap = AFOverlap,
 stats = "median", ExportType = "data", SignatureReturnNow = FALSE,
 outpath = TemporaryFolder, Increments=0.1, SecondaryPeaks=2,
 experiment = "FirstExperiment", condition = "ILTPanel", Subtraction = "Internal",
 CellAF=TheCellAF, SCData="subtracted", NegativeType="default") %>% bind_rows()