#Christopher Hall, Wellcome Sanger Institute, [email protected]

#Bulk export of ARIA index information V3. Now with added flowsetieness and 384 well plate support

#load the required packages from BioConductor

source("https://bioconductor.org/biocLite.R")

biocLite("flowCore")

library(flowCore)

#Change setwd to the directory of your folder

setwd("C:/Users/ch15/Desktop/files")

#run these lines and csv files will be produced using the included compensation matrix for each file

files <- list.files(path=".", pattern=".fcs$") #list files in directory the $ means it must end with .fcs

fs<-read.flowSet(files, transformation = FALSE) #puts all the .fcs files into a flowset

fsApply(fs,function(frame){ #loop through the flowset

comp <- keyword(frame)$SPILL #take the compensation matrix, remove 16+17 for uncompensated data

new_frame <- compensate(frame,comp) #apply the comepensation matrix

editme<- data.frame(getIndexSort(new_frame)) #get the index data and convert to a data.frame to help with the WellID (new_frame -> frame if not compensating)

editme$XLoc<-chartr("0", "A", editme$XLoc) #replace '0' with 'A' because setNames seems to not work with 0 with a really odd error

editme$WellID<-setNames(c("A","B","C","D","E","F","G","H","I","J","K","L","M","N","N","P"), c("A","1","2","3","4","5","6","7","8","9","10","11","12","13","14","15"))[editme$XLoc] #use setNames to rename the XLoc positions with well names

editme$XLoc<-chartr("A", "0", editme$XLoc) # #restore original XLoc '0' name

editme$WellID<-paste(editme$WellID,editme$YLoc +1, sep="") #add one to each YLoc to match the plate designations

write.csv(editme, file=paste(keyword(new_frame,"GUID"), "_index.csv", sep="")) #write a csv using the GUID keyword as the filename

})