quick launcher and tester for rna-seq_analysis with the FNR study case

scripts/RSnakeChunks/misc/FNR_analysis_test.R

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+## Test to run the RNA-seq_analysis.R script in interactive R interface, with the FNR analysis study case
+##
+##
+## Equivalent ommand-line
+## Rscript --vanilla  SnakeChunks/scripts/RSnakeChunks/misc/rna-seq_deg.R -v 1 \
+##    --config_file=metadata/config_RNA-seq.yml  \
+##    --count_table=RNA-seq/results/diffexpr/cutadapt_bwa_featureCounts_all.tsv  \
+##    --output_dir=RNA-seq/results/diffexpr/  \
+##    --rsnakechunks_dir=SnakeChunks/scripts/RSnakeChunks  \
+##    --report RNA-seq/results/diffexpr/cutadapt_bwa_featureCounts_rna-seq_deg_report.Rmd  \
+##    &> RNA-seq/results/diffexpr/cutadapt_bwa_featureCounts_rna-seq_deg.log
+
+analysis.dir <- '~/FNR_analysis/'
+
+setwd(analysis.dir)
+
+opt <- list(
+  main_dir = analysis.dir,
+  config_file = "metadata/config_RNA-seq.yml",
+  count_table = "RNA-seq/results/diffexpr/cutadapt_bwa_featureCounts_all.tsv",
+  rsnakechunks_dir = "SnakeChunks/scripts/RSnakeChunks",
+  output_dir  = "RNA-seq/results/diffexpr/",
+  rmd_report  = "RNA-seq/results/diffexpr/cutadapt_bwa_featureCounts_rna-seq_deg_report.Rmd",
+  verbose = 1
+)
+
+
+
+## ----  Load R functions from SnakeChunks directory if specified ----
+if ((!is.null(opt$snakechunks_dir)) & (is.null(opt$rsnakechunks_dir))) {
+  opt$rsnakechunks_dir <- file.path(opt$snakechunks_dir, "scripts", "RSnakeChunks")
+}
+if (!is.null(opt$rsnakechunks_dir)) {
+  message("Reading R functions from RSnakeChunks\t", opt$SnakeChunks)
+
+  ## NOTE: if the RSnakechunks package has been compiled on this machine
+  ## the functions will be loaded with library('RSnakeChunks'). However
+  ## for the ime being we do not assume that RSnakeChunks has been
+  ## compiled with SnakeChunks installation, so we souce all the files
+  ## containing R functions.
+  R.dir <- file.path(opt$rsnakechunks, "R")
+  message("R directory\t", R.dir)
+  R.files <- list.files(R.dir)
+  for (f in R.files) {
+    message("\tLoading R file ", f)
+    source(file.path(R.dir, f))
+  }
+}
+
+## ---- Run the analysis ----
+RNAseqAnalysis(
+  countFile = opt$count_table,
+  configFile = opt$config_file,
+  main.dir = opt$main_dir,
+  result.dir = opt$output_dir,
+  rmd.report = opt$rmd_report,
+  verbose = opt$verbose)