Concatenate a gs based on subset and optional subsample

Usage

Utility_Concatinate(
  gs,
  sample.name,
  removestrings,
  subsets,
  subsample = NULL,
  ReturnType,
  newName,
  outpath = NULL,
  export = FALSE,
  inverse.transform = FALSE
)

Arguments

gs: A gating set object
sample.name: Keyword specifying sample name
removestrings: Value to be removed from sample name
subsets: The gating hierarchy subset you want to include
subsample: Default is set to NULL. If down-sample is desired, Total number of events to subsample from each specimen
ReturnType: Whether to return as a "data.frame", a "flow.frame", or export to an "fcs" file to the outpath location
newName: File Name for the Concatenate File
outpath: Location to store the concatenated file
export: Whether to export as a .fcs file.
inverse.transform: Whether to reverse the GatingSet Transform on the data, default is set to FALSE.

Value

A concatenated data.frame, flow.frame or fcs file, with reference .csv for the specimen information

Examples


library(BiocGenerics)
library(flowCore)
library(flowWorkspace)
library(openCyto)
library(data.table)

File_Location <- system.file("extdata", package = "Luciernaga")
FCS_Files <- list.files(path = File_Location, pattern = ".fcs",
  full.names = TRUE)
Unmixed_FullStained <- FCS_Files[grep("Unmixed", FCS_Files)]
UnmixedFCSFiles <- Unmixed_FullStained[1:2]
UnmixedCytoSet <- load_cytoset_from_fcs(UnmixedFCSFiles[1:2],
  truncate_max_range = FALSE,transformation = FALSE)
UnmixedGatingSet <- GatingSet(UnmixedCytoSet)
Markers <- colnames(UnmixedCytoSet)
KeptMarkers <- Markers[-grep("Time|FS|SC|SS|Original|-W$|-H$|AF", Markers)]
MyBiexponentialTransform <- flowjo_biexp_trans(channelRange = 256,
  maxValue = 1000000,pos = 4.5, neg = 0, widthBasis = -1000)
TransformList <- transformerList(KeptMarkers, MyBiexponentialTransform)
UnmixedGatingSet <- flowWorkspace::transform(UnmixedGatingSet, TransformList)
FileLocation <- system.file("extdata", package = "Luciernaga")
UnmixedGates <- fread(file.path(path = FileLocation, pattern = 'GatesUnmixed.csv'))
UnmixedGating <- gatingTemplate(UnmixedGates)
#> Adding population:singletsFSC
#> Adding population:singletsSSC
#> Adding population:singletsSSCB
#> Adding population:nonDebris
#> Adding population:lymphocytes
#> Adding population:live
gt_gating(UnmixedGating, UnmixedGatingSet)
#> 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.
#> Gating for 'live'
#> done!
#> done.
#> finished.

removestrings <-  c("DTR_", ".fcs")
StorageLocation <- file.path("C:", "Users", "JohnDoe", "Desktop")

ConcatinatedReturn <- Utility_Concatinate(gs=UnmixedGatingSet,
  sample.name = "GROUPNAME", removestrings=removestrings,
  subsets="live", subsample = 2000, ReturnType = "flow.frame",
  newName = "MyConcatinatedFile", outpath = StorageLocation, export = FALSE)
#> INF071 has been processed
#> INF149 has been processed