Bug fixes.

.gitignore

+debugging_v2.2/

V2.2/run_analysis.sh

 #!/bin/bash
-module load singularity/3.9.9
+module load singularity/3.9.9	#Change this to your own command if required for running singularity on your computer.
 ODA_DIR=$1
 ODA_MODULE=$ODA_DIR/r_with_packages_4.3.2.sif	#Link to: /archive/CRI/shared/Singularity/zzy/r_w_packages_4.3.2.sif
 INPUT_FILE=$2
 OUTPUT_FOLDER=$3
 echo $ODA_MODULE
-singularity exec $ODA_MODULE Rscript $ODA_DIR/ODA/ODA.R $INPUT_FILE $OUTPUT_FOLDER 2>&1 | tee -a "$OUTPUT_FOLDER/ODA_run"$(date +%s"."%N)".log"
+singularity exec $ODA_MODULE Rscript /ODA/ODA.R $INPUT_FILE $OUTPUT_FOLDER 2>&1 | tee -a "$OUTPUT_FOLDER/ODA_run"$(date +%s"."%N)".log"
 

debugging_v2.2/test/EnrichmentAnalysis/go-mf_clusterprofiler-qea/clusterprofiler_qea.csv

 "ID","Description","setSize","enrichmentScore","NES","pvalue","p.adjust","qvalue","rank","leading_edge","core_enrichment"
-"GO:0004672","MF_protein kinase activity",3,0.947368421052632,1.67880723278115,0.00469923405460483,0.0146851064206401,0.00927480405514111,4,"tags=100%, list=18%, signal=95%","IGF1R/PDGFRA/MET"
-"GO:0004713","MF_protein tyrosine kinase activity",3,0.947368421052632,1.67880723278115,0.00469923405460483,0.0146851064206401,0.00927480405514111,4,"tags=100%, list=18%, signal=95%","IGF1R/PDGFRA/MET"
-"GO:0004714","MF_transmembrane receptor protein tyrosine kinase activity",3,0.947368421052632,1.67880723278115,0.00469923405460483,0.0146851064206401,0.00927480405514111,4,"tags=100%, list=18%, signal=95%","IGF1R/PDGFRA/MET"
-"GO:0004888","MF_transmembrane signaling receptor activity",3,0.947368421052632,1.67880723278115,0.00469923405460483,0.0146851064206401,0.00927480405514111,4,"tags=100%, list=18%, signal=95%","IGF1R/PDGFRA/MET"
-"GO:0005524","MF_ATP binding",3,0.947368421052632,1.67880723278115,0.00469923405460483,0.0146851064206401,0.00927480405514111,4,"tags=100%, list=18%, signal=95%","IGF1R/PDGFRA/MET"
-"GO:0016301","MF_kinase activity",3,0.947368421052632,1.67880723278115,0.00469923405460483,0.0146851064206401,0.00927480405514111,4,"tags=100%, list=18%, signal=95%","IGF1R/PDGFRA/MET"
-"GO:0016740","MF_transferase activity",3,0.947368421052632,1.67880723278115,0.00469923405460483,0.0146851064206401,0.00927480405514111,4,"tags=100%, list=18%, signal=95%","IGF1R/PDGFRA/MET"
-"GO:0016772","MF_transferase activity, transferring phosphorus-containing groups",3,0.947368421052632,1.67880723278115,0.00469923405460483,0.0146851064206401,0.00927480405514111,4,"tags=100%, list=18%, signal=95%","IGF1R/PDGFRA/MET"
-"GO:0016773","MF_phosphotransferase activity, alcohol group as acceptor",3,0.947368421052632,1.67880723278115,0.00469923405460483,0.0146851064206401,0.00927480405514111,4,"tags=100%, list=18%, signal=95%","IGF1R/PDGFRA/MET"
-"GO:0019199","MF_transmembrane receptor protein kinase activity",3,0.947368421052632,1.67880723278115,0.00469923405460483,0.0146851064206401,0.00927480405514111,4,"tags=100%, list=18%, signal=95%","IGF1R/PDGFRA/MET"
-"GO:0030554","MF_adenyl nucleotide binding",3,0.947368421052632,1.67880723278115,0.00469923405460483,0.0146851064206401,0.00927480405514111,4,"tags=100%, list=18%, signal=95%","IGF1R/PDGFRA/MET"
-"GO:0032559","MF_adenyl ribonucleotide binding",3,0.947368421052632,1.67880723278115,0.00469923405460483,0.0146851064206401,0.00927480405514111,4,"tags=100%, list=18%, signal=95%","IGF1R/PDGFRA/MET"
-"GO:0038023","MF_signaling receptor activity",3,0.947368421052632,1.67880723278115,0.00469923405460483,0.0146851064206401,0.00927480405514111,4,"tags=100%, list=18%, signal=95%","IGF1R/PDGFRA/MET"
-"GO:0060089","MF_molecular transducer activity",3,0.947368421052632,1.67880723278115,0.00469923405460483,0.0146851064206401,0.00927480405514111,4,"tags=100%, list=18%, signal=95%","IGF1R/PDGFRA/MET"
-"GO:0140096","MF_catalytic activity, acting on a protein",3,0.947368421052632,1.67880723278115,0.00469923405460483,0.0146851064206401,0.00927480405514111,4,"tags=100%, list=18%, signal=95%","IGF1R/PDGFRA/MET"
-"GO:0098772","MF_molecular function regulator activity",20,-1,-1.57862708997319,0.00465806923372689,0.0146851064206401,0.00927480405514111,21,"tags=100%, list=95%, signal=50%","MET/PDGFC/FGF16/FGF18/PDGFA/FGF23/IGF1/FGF7/HGF/PDGFB/KRAS/FGF17/FGF1/PDGFD/FGF4/FGF10/HRAS/FGF8/FGF9"
+"GO:0004672","MF_protein kinase activity",3,0.947368421052632,1.71714885655643,0.0118680559020671,0.0370876746939597,0.0234237945435535,4,"tags=100%, list=18%, signal=95%","IGF1R/PDGFRA/MET"
+"GO:0004713","MF_protein tyrosine kinase activity",3,0.947368421052632,1.71714885655643,0.0118680559020671,0.0370876746939597,0.0234237945435535,4,"tags=100%, list=18%, signal=95%","IGF1R/PDGFRA/MET"
+"GO:0004714","MF_transmembrane receptor protein tyrosine kinase activity",3,0.947368421052632,1.71714885655643,0.0118680559020671,0.0370876746939597,0.0234237945435535,4,"tags=100%, list=18%, signal=95%","IGF1R/PDGFRA/MET"
+"GO:0004888","MF_transmembrane signaling receptor activity",3,0.947368421052632,1.71714885655643,0.0118680559020671,0.0370876746939597,0.0234237945435535,4,"tags=100%, list=18%, signal=95%","IGF1R/PDGFRA/MET"
+"GO:0005524","MF_ATP binding",3,0.947368421052632,1.71714885655643,0.0118680559020671,0.0370876746939597,0.0234237945435535,4,"tags=100%, list=18%, signal=95%","IGF1R/PDGFRA/MET"
+"GO:0016301","MF_kinase activity",3,0.947368421052632,1.71714885655643,0.0118680559020671,0.0370876746939597,0.0234237945435535,4,"tags=100%, list=18%, signal=95%","IGF1R/PDGFRA/MET"
+"GO:0016740","MF_transferase activity",3,0.947368421052632,1.71714885655643,0.0118680559020671,0.0370876746939597,0.0234237945435535,4,"tags=100%, list=18%, signal=95%","IGF1R/PDGFRA/MET"
+"GO:0016772","MF_transferase activity, transferring phosphorus-containing groups",3,0.947368421052632,1.71714885655643,0.0118680559020671,0.0370876746939597,0.0234237945435535,4,"tags=100%, list=18%, signal=95%","IGF1R/PDGFRA/MET"
+"GO:0016773","MF_phosphotransferase activity, alcohol group as acceptor",3,0.947368421052632,1.71714885655643,0.0118680559020671,0.0370876746939597,0.0234237945435535,4,"tags=100%, list=18%, signal=95%","IGF1R/PDGFRA/MET"
+"GO:0019199","MF_transmembrane receptor protein kinase activity",3,0.947368421052632,1.71714885655643,0.0118680559020671,0.0370876746939597,0.0234237945435535,4,"tags=100%, list=18%, signal=95%","IGF1R/PDGFRA/MET"
+"GO:0030554","MF_adenyl nucleotide binding",3,0.947368421052632,1.71714885655643,0.0118680559020671,0.0370876746939597,0.0234237945435535,4,"tags=100%, list=18%, signal=95%","IGF1R/PDGFRA/MET"
+"GO:0032559","MF_adenyl ribonucleotide binding",3,0.947368421052632,1.71714885655643,0.0118680559020671,0.0370876746939597,0.0234237945435535,4,"tags=100%, list=18%, signal=95%","IGF1R/PDGFRA/MET"
+"GO:0038023","MF_signaling receptor activity",3,0.947368421052632,1.71714885655643,0.0118680559020671,0.0370876746939597,0.0234237945435535,4,"tags=100%, list=18%, signal=95%","IGF1R/PDGFRA/MET"
+"GO:0060089","MF_molecular transducer activity",3,0.947368421052632,1.71714885655643,0.0118680559020671,0.0370876746939597,0.0234237945435535,4,"tags=100%, list=18%, signal=95%","IGF1R/PDGFRA/MET"
+"GO:0140096","MF_catalytic activity, acting on a protein",3,0.947368421052632,1.71714885655643,0.0118680559020671,0.0370876746939597,0.0234237945435535,4,"tags=100%, list=18%, signal=95%","IGF1R/PDGFRA/MET"
+"GO:0098772","MF_molecular function regulator activity",20,-1,-1.57370997622202,0.0023378689421659,0.0370876746939597,0.0234237945435535,21,"tags=100%, list=95%, signal=50%","MET/PDGFC/FGF16/FGF18/PDGFA/FGF23/IGF1/FGF7/HGF/PDGFB/KRAS/FGF17/FGF1/PDGFD/FGF4/FGF10/HRAS/FGF8/FGF9"