Added bioconductor and fix spelling

FCS-to-CSV v2.0.R

@@ -1,79 +1,82 @@
 # FCS to CSV
-    # Coverting .fcs file data into an .csv file
-    # Thomas Ashhurst
-    # 2017-09-13
-    # github.com/sydneycytometry
-    # .fcs file reading and writing adapted from https://gist.github.com/yannabraham/c1f9de9b23fb94105ca5
+# Coverting .fcs file data into an .csv file
+# Thomas Ashhurst
+# 2017-09-13
+# github.com/sydneycytometry
+# .fcs file reading and writing adapted from https://gist.github.com/yannabraham/c1f9de9b23fb94105ca5
 
 
 ##### USER INPUT #####
-
-    # Install packages if required
-    if(!require('flowCore')) {install.packages('flowCore')}
-    if(!require('Biobase')) {install.packages('Biobase')}
-    if(!require('data.table')) {install.packages('data.table')}
-
-    # Load packages
-    library('flowCore')
-    library('Biobase')
-    library('data.table')
-
-    # In order for this to work, a) rstudioapi must be installed and b) the location of this .r script must be in your desired working directory
-    dirname(rstudioapi::getActiveDocumentContext()$path)            # Finds the directory where this script is located
-    setwd(dirname(rstudioapi::getActiveDocumentContext()$path))     # Sets the working directory to where the script is located
-    getwd()
-    PrimaryDirectory <- getwd()
-    PrimaryDirectory
-
-    # Use this to manually set the working directory
-    #setwd("/Users/Tom/Desktop/Experiment")                          # Set your working directory here (e.g. "/Users/Tom/Desktop/") -- press tab when selected after the '/' to see options
-    #getwd()                                                         # Check your working directory has changed correctly
-    #PrimaryDirectory <- getwd()                                     # Assign the working directory as 'PrimaryDirectory'
-    #PrimaryDirectory
-
-    ## Use to list the .csv files in the working directory -- important, the only CSV files in the directory should be the one desired for analysis. If more than one are found, only the first file will be used
-    FileNames <- list.files(path=PrimaryDirectory, pattern = ".fcs")     # see a list of CSV files
-    as.matrix(FileNames) # See file names in a list
-
-    ## Read data from Files into list of data frames
-    DataList=list() # Creates and empty list to start 
-
-    for (File in FileNames) { # Loop to read files into the list
-      tempdata <- exprs(read.FCS(File, transformation = FALSE))
-      tempdata <- tempdata[1:nrow(tempdata),1:ncol(tempdata)]
-      File <- gsub(".fcs", "", File)
-      DataList[[File]] <- tempdata
-    }
-
-    rm(tempdata)
-    AllSampleNames <- names(DataList)
-
-    ## Chech data quality
-    head(DataList)
-
-
-
+
+# Install packages if required using Bioconductor
+if (!requireNamespace("BiocManager", quietly = TRUE))
+  install.packages("BiocManager")
+BiocManager::install("flowCore")
+BiocManager::install("Biobase")
+
+# Install packages if required using standard installation
+if(!require('data.table')) {install.packages('data.table')}
+
+# Load packages
+library('flowCore')
+library('Biobase')
+library('data.table')
+
+# In order for this to work, a) rstudioapi must be installed and b) the location of this .r script must be in your desired working directory
+dirname(rstudioapi::getActiveDocumentContext()$path)            # Finds the directory where this script is located
+setwd(dirname(rstudioapi::getActiveDocumentContext()$path))     # Sets the working directory to where the script is located
+getwd()
+PrimaryDirectory <- getwd()
+PrimaryDirectory
+
+# Use this to manually set the working directory
+#setwd("/Users/Tom/Desktop/")                          # Set your working directory here (e.g. "/Users/Tom/Desktop/") -- press tab when selected after the '/' to see options
+#getwd()                                                         # Check your working directory has changed correctly
+#PrimaryDirectory <- getwd()                                     # Assign the working directory as 'PrimaryDirectory'
+#PrimaryDirectory
+
+## Use to list the .fcs files in the working directory -- important, the only FCS files in the directory should be the one desired for analysis. If more than one are found, only the first file will be used
+FileNames <- list.files(path=PrimaryDirectory, pattern = ".fcs")     # see a list of FCS files
+as.matrix(FileNames) # See file names in a list
+
+## Read data from Files into list of data frames
+DataList=list() # Creates and empty list to start 
+
+for (File in FileNames) { # Loop to read files into the list
+  tempdata <- exprs(read.FCS(File, transformation = FALSE))
+  tempdata <- tempdata[1:nrow(tempdata),1:ncol(tempdata)]
+  File <- gsub(".fcs", "", File)
+  DataList[[File]] <- tempdata
+}
+
+rm(tempdata)
+AllSampleNames <- names(DataList)
+
+## Chech data quality
+head(DataList)
+
+
+
 ##### END USER INPUT #####
-
-    x <- Sys.time()
-    x <- gsub(":", "-", x)
-    x <- gsub(" ", "_", x)
-
-    newdir <- paste0("Output_FCS-to-CSV", "_", x)
-
-    setwd(PrimaryDirectory)
-    dir.create(paste0(newdir), showWarnings = FALSE)
-    setwd(newdir)
-
-
-    for(i in c(1:length(AllSampleNames))){
-      data_subset <- DataList[i][[1]]
-      data_subset <- as.data.frame(data_subset)
-      colnames(data_subset)
-      #data_subset <- rbindlist(as.list(data_subset$sample_data))
-      dim(data_subset)
-      a <- names(DataList)[i]
-
-      write.csv(data_subset, paste0(a, ".csv"))
-    }
-
+
+x <- Sys.time()
+x <- gsub(":", "-", x)
+x <- gsub(" ", "_", x)
+
+newdir <- paste0("Output_FCS-to-CSV", "_", x)
+
+setwd(PrimaryDirectory)
+dir.create(paste0(newdir), showWarnings = FALSE)
+setwd(newdir)
+
+
+for(i in c(1:length(AllSampleNames))){
+  data_subset <- DataList[i][[1]]
+  data_subset <- as.data.frame(data_subset)
+  colnames(data_subset)
+  #data_subset <- rbindlist(as.list(data_subset$sample_data))
+  dim(data_subset)
+  a <- names(DataList)[i]
+
+  write.csv(data_subset, paste0(a, ".csv"))
+}