Refactoring step 04 to process all datasets at once (Second part - after match).

04-Prepare_datasets/Makefile

@@ -15,7 +15,5 @@ ps:
 	@sbatch ${CODE_FOLDER}create_probelists.sh
 match:
 	@sbatch ${CODE_FOLDER}match_probes.sh
-biomarker:
-	@sbatch ${CODE_FOLDER}plot_biomarkers.sh
 doc:
-	@sbatch ${CODE_FOLDER}doc.sh
+	@sbatch ${CODE_FOLDER}doc.sh
\ No newline at end of file

04-Prepare_datasets/doc.sh

@@ -122,29 +122,11 @@ do
 	echo '	}' >> ${OUTPUT_FOLDER}results_summary.tex
 	echo '\end{figure}' >> ${OUTPUT_FOLDER}results_summary.tex
 	echo '' >> ${OUTPUT_FOLDER}results_summary.tex
-done
-
-echo '\clearpage' >> ${OUTPUT_FOLDER}results_summary.tex
-echo '' >> ${OUTPUT_FOLDER}results_summary.tex
-
 
-# Per biomarker analysis.
-nbBiomarkers=${#biomarkers__name[@]}
-for (( i=0; i<$nbBiomarkers; i++ ))
-do
-	biomarkerName=${biomarkers__name[$i]}
-	biomarkerTissue=${biomarkers__tissue[$i]}
-	biomarkerTissueForFile=${biomarkerTissue/ /_}
-	echo '\begin{figure}[ht]' >> ${OUTPUT_FOLDER}results_summary.tex
-	echo '	\centering' >> ${OUTPUT_FOLDER}results_summary.tex
-	echo '	\includegraphics[scale=0.43]{'"$OUTPUT_FOLDER"'Biomarker_'"${biomarkerTissueForFile}"'_'"${biomarkerName}"'.png}' >> ${OUTPUT_FOLDER}results_summary.tex
-	echo '	\caption{Expression values for biomarker '"${biomarkerName}"' for both DA and SN tissues.' >> ${OUTPUT_FOLDER}results_summary.tex
-	echo '	(Top) Usage of expression values as derived from pre-processing. (Bottom) Usage of Z-scores ' >> ${OUTPUT_FOLDER}results_summary.tex
-	echo '	derived from the expression values. (Left) VSN correction applied. (Right) No VSN correction applied.}' >> ${OUTPUT_FOLDER}results_summary.tex
-	echo '\end{figure}' >> ${OUTPUT_FOLDER}results_summary.tex
+	echo '\clearpage' >> ${OUTPUT_FOLDER}results_summary.tex
 	echo '' >> ${OUTPUT_FOLDER}results_summary.tex
-done
 
+done
 
 # Print footer
 echo '' >> ${OUTPUT_FOLDER}results_summary.tex

04-Prepare_datasets/match_probes.R

@@ -377,7 +377,8 @@ for (i in seq_len(length(config$platforms))) {
     dplyr::rename(!!platform$platform_name := probesets)
   rm(deps_matching, matching_dataset, platform)
 } # End for each platform.
-rm(i, genes_probe_matching, geneset_probe_matching)
+#rm(i, genes_probe_matching, geneset_probe_matching)
+rm(i)
 
 # We merge the dataframes, create one global matching dataframe and save it.
 global_matching_data_merged <- NULL