Summarize a data.frame to desired stat

Usage

AveragedSignature(x, stats)

Arguments

x: A data.frame containing double or numeric data.
stats: Desired Stats "mean" or "median" to pass to summarize_all

Value

A data.frame row of summarized data

Examples


library(flowCore)
library(flowWorkspace)
#> As part of improvements to flowWorkspace, some behavior of
#> GatingSet objects has changed. For details, please read the section
#> titled "The cytoframe and cytoset classes" in the package vignette:
#> 
#>   vignette("flowWorkspace-Introduction", "flowWorkspace")
library(openCyto)
library(data.table)
#> data.table 1.16.2 using 4 threads (see ?getDTthreads).  
#> Latest news: r-datatable.com

File_Location <- system.file("extdata", package = "Luciernaga")
FCS_Files <- list.files(path = File_Location, pattern = ".fcs",
  full.names = TRUE)
UnstainedFCSFiles <- FCS_Files[grep("Unstained", FCS_Files)]
UnstainedCells <- UnstainedFCSFiles[-grep("Beads", UnstainedFCSFiles)]
MyCytoSet <- load_cytoset_from_fcs(UnstainedCells[1],
  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
#> done!
#> done.
#> finished.
removestrings <-  c("DR_", "Cells", ".fcs", "-", " ")
StorageLocation <- file.path("C:", "Users", "JohnDoe", "Desktop")

PopulationInterest <- gs_pop_get_data(MyGatingSet[1], subset="lymphocytes")
TheDataValues <- exprs(PopulationInterest[[1]])
TheDataValues <- data.frame(TheDataValues, check.names=FALSE)

Signature <- AveragedSignature(TheDataValues, stats="median")