BatchFlowType.R

#!/usr/bin/env Rscript

require(docopt)
require(methods)

"
Usage:
BatchFlowType.R (-h | --help | --version)
BatchFlowType.R DIR

Description:   This script applies the flowType algorthim to high parameter cytometry data
Options:
--version       Show the current version.

Arguments:

DIR    Provide directory for cytools.args.Rdata to be found, automatically generated by invoking cyttools.R
" -> doc


args <- docopt(doc)

cat(args$DIR, "\n", args$OUT, "\n")

ARGS_DIR <- args$DIR

ARGS_DIR <- gsub("DataPrepWorkspace\\_.*", "Results/", ARGS_DIR)

ARGS_FILE <- paste(ARGS_DIR, "cyttools.args.Rdata", sep = "")

cat("\nLOADING ARGUEMENTS:", ARGS_FILE, "\n")

load(ARGS_FILE)

RESULTS_DIR <- args$OUT

cat("\nResults will be written to", RESULTS_DIR, "\n")

source("cyttoolsFunctions.R")

file <- args$DIR # grabs directory from initial cyttools call

load(file)

ResList <- flowType(ffb,
                    MarkerNames = parameters(ffb)$desc,
                    MemLimit = 15)

workspaceFile <- paste(RESULTS_DIR,
                       gsub(gsub("BatchFlowTypeResults/", "", RESULTS_DIR),
                            "",
                            file), sep = "")

save(ResList, file = workspaceFile)