Commit d7b41601 authored by Leon-Charles Tranchevent's avatar Leon-Charles Tranchevent
Browse files

Added code to select the most interesting interactions from given regulatory...

Added code to select the most interesting interactions from given regulatory networks (based on differential expression data and consistency with knowledge databases).
parent c9b5b26b
......@@ -33,13 +33,16 @@ refineGRN1:
@echo "* LOCATED IN THE DATA FOLDER. MISSING GENES SHOULD BE DOUBLE CHECKED IN *"
@echo "* GENEGO. *"
@echo "********************************************************************************"
# End of "From now on, we need GeneGo results".
refineGRN2:
@sbatch ${CODE_FOLDER}refine_GRN.sh
refineEnrich:
@sbatch ${CODE_FOLDER}refine_enrich.sh
prepCarnival:
@sbatch ${CODE_FOLDER}prepare_carnival.sh
runCarnival:
@sbatch ${CODE_FOLDER}run_carnival.sh
refineCarnival:
@sbatch ${CODE_FOLDER}refine_carnival.sh
#prepCarnival:
# @sbatch ${CODE_FOLDER}prepare_carnival.sh
#runCarnival:
# @sbatch ${CODE_FOLDER}run_carnival.sh
#refineCarnival:
# @sbatch ${CODE_FOLDER}refine_carnival.sh
selectInts:
@sbatch ${CODE_FOLDER}select_interactions.sh
This diff is collapsed.
#!/bin/bash -l
#SBATCH -J geneder:18:carnival
#SBATCH --mail-type=all
#SBATCH --mail-user=leon-charles.tranchevent@uni.lu
#SBATCH -N 1
#SBATCH -n 10
#SBATCH --time=0-01:00:00
#SBATCH -p batch
#SBATCH --qos=qos-batch
echo "== Starting run at $(date)"
echo "== Job ID: ${SLURM_JOBID}"
echo "== Node list: ${SLURM_NODELIST}"
echo "== Submit dir. : ${SLURM_SUBMIT_DIR}"
echo ""
# Loading modules.
module load lang/R/3.6.0-foss-2019a-bare
module load math/CPLEX/12.9-foss-2019a
# Defining global parameters.
INPUT_FOLDER=/home/leon/Projects/GeneDER/Results/Regulatory_v05/Refined/
OUTPUT_FOLDER=/home/users/ltranchevent/Data/GeneDER/Analysis/18/
CODE_FOLDER=/home/users/ltranchevent/Projects/GeneDER/Analysis/18-RegulatoryNetwork_all/
# Copy the data locally (teh manually refined GeneGO and DoRothEA files).
cp ${INPUT_FOLDER}SNage_VSN_PDVsControl_all_lists_*_GRN_internal_refined.tsv ${OUTPUT_FOLDER}
cp ${INPUT_FOLDER}SelectedTFs_* ${OUTPUT_FOLDER}
# Actual job in R.
Rscript --vanilla ${CODE_FOLDER}select_interactions.R > ${OUTPUT_FOLDER}select_ints_log.out 2> ${OUTPUT_FOLDER}select_ints_log.err
# We concatenate the individual files to create the global files.
head -n 1 ${OUTPUT_FOLDER}*dorothea*annotations.tsv > ${OUTPUT_FOLDER}SNage_VSN_PDVsControl_all_lists_global_GRN_internal_refined_selected_annotations.tsv
cat ${OUTPUT_FOLDER}*annotations* | grep -v Gene | sort -u >> ${OUTPUT_FOLDER}SNage_VSN_PDVsControl_all_lists_global_GRN_internal_refined_selected_annotations.tsv
cat ${OUTPUT_FOLDER}*_network.sif | sort -u > ${OUTPUT_FOLDER}SNage_VSN_PDVsControl_all_lists_global_GRN_internal_refined_selected_network.sif
# Moving the slurm log file to data
mv ${CODE_FOLDER}/slurm-*out ${OUTPUT_FOLDER}/
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