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adding shellscripts for power version of wgcna, and pr shellscripts
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| #!/bin/sh | ||
| #SBATCH --time=26:0:0 | ||
| #SBATCH --mem=80G | ||
| #SBATCH --partition=shared | ||
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| source ~/.bash_profile | ||
| source /work-zfs/abattle4/parsana/networks_correction/shellscripts/dirconfig | ||
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| cd $scriptDir | ||
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| Rscript compute_pr.R Subcutaneous $datDir/genesets/canonical_pathways_merged.txt $plotDir $resultDir canonical_subcutaneous power_wgcna FALSE >$logDir/pr_canonical_power_wgcna_subcutaneous.log | ||
| Rscript compute_pr.R Lung $datDir/genesets/canonical_pathways_merged.txt $plotDir $resultDir canonical_lung power_wgcna FALSE >$logDir/pr_canonical_power_wgcna_lung.log | ||
| Rscript compute_pr.R Thyroid $datDir/genesets/canonical_pathways_merged.txt $plotDir $resultDir canonical_thyroid power_wgcna FALSE >$logDir/pr_canonical_power_wgcna_thyroid.log | ||
| Rscript compute_pr.R Muscle $datDir/genesets/canonical_pathways_merged.txt $plotDir $resultDir canonical_muscle power_wgcna FALSE >$logDir/pr_canonical_power_wgcna_muscle.log | ||
| Rscript compute_pr.R Blood $datDir/genesets/canonical_pathways_merged.txt $plotDir $resultDir canonical_blood power_wgcna FALSE >$logDir/pr_canonical_power_wgcna_blood.log | ||
| Rscript compute_pr.R Artery_tibial $datDir/genesets/canonical_pathways_merged.txt $plotDir $resultDir canonical_artery power_wgcna FALSE >$logDir/pr_canonical_pathways_merged_power_wgcna_srtery.log | ||
| Rscript compute_pr.R Nerve_tibial $datDir/genesets/canonical_pathways_merged.txt $plotDir $resultDir canonical_nerve power_wgcna FALSE >$logDir/pr_canonical_pathways_merged_power_wgcna_nerve.log | ||
| Rscript compute_pr.R Skin $datDir/genesets/canonical_pathways_merged.txt $plotDir $resultDir canonical_skin power_wgcna FALSE >$logDir/pr_canonical_pathways_merged_power_wgcna_skin.log | ||
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| Rscript compute_pr.R Subcutaneous $datDir/genesets/tft.txt $plotDir $resultDir tft_subcutaneous power_wgcna FALSE >$logDir/pr_tft_power_wgcna_subcutaneous.log | ||
| Rscript compute_pr.R Lung $datDir/genesets/tft.txt $plotDir $resultDir tft_lung power_wgcna FALSE >$logDir/pr_tft_power_wgcna_lung.log | ||
| Rscript compute_pr.R Thyroid $datDir/genesets/tft.txt $plotDir $resultDir tft_thyroid power_wgcna FALSE >$logDir/pr_tft_power_wgcna_thyroid.log | ||
| Rscript compute_pr.R Muscle $datDir/genesets/tft.txt $plotDir $resultDir tft_muscle power_wgcna FALSE >$logDir/pr_tft_power_wgcna_muscle.log | ||
| Rscript compute_pr.R Blood $datDir/genesets/tft.txt $plotDir $resultDir tft_blood power_wgcna FALSE >$logDir/pr_tft_power_wgcna_blood.log | ||
| Rscript compute_pr.R Artery_tibial $datDir/genesets/tft.txt $plotDir $resultDir tft_artery power_wgcna FALSE >$logDir/pr_tft_power_wgcna_srtery.log | ||
| Rscript compute_pr.R Nerve_tibial $datDir/genesets/tft.txt $plotDir $resultDir tft_nerve power_wgcna FALSE >$logDir/pr_tft_power_wgcna_nerve.log | ||
| Rscript compute_pr.R Skin $datDir/genesets/tft.txt $plotDir $resultDir tft_skin power_wgcna FALSE >$logDir/pr_tft_power_wgcna_skin.log |
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,32 @@ | ||
| #!/bin/sh | ||
| #SBATCH --time=46:0:0 | ||
| #SBATCH --mem=80G | ||
| #SBATCH --partition=shared | ||
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| source ~/.bash_profile | ||
| source /work-zfs/abattle4/parsana/networks_correction/shellscripts/dirconfig | ||
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| cd $scriptDir | ||
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| Rscript compute_pr.R Subcutaneous $datDir/genesets/edges_in_twopathways.txt $plotDir $resultDir shared_subcutaneous wgcna-signed TRUE >$logDir/pr_shared_wgcna-signed_subcutaneous.log | ||
| Rscript compute_pr.R Lung $datDir/genesets/edges_in_twopathways.txt $plotDir $resultDir shared_lung wgcna-signed TRUE >$logDir/pr_shared_wgcna-signed_lung.log | ||
| Rscript compute_pr.R Thyroid $datDir/genesets/edges_in_twopathways.txt $plotDir $resultDir shared_thyroid wgcna-signed TRUE >$logDir/pr_shared_wgcna-signed_thyroid.log | ||
| Rscript compute_pr.R Muscle $datDir/genesets/edges_in_twopathways.txt $plotDir $resultDir shared_muscle wgcna-signed TRUE >$logDir/pr_shared_wgcna-signed_muscle.log | ||
| Rscript compute_pr.R Blood $datDir/genesets/edges_in_twopathways.txt $plotDir $resultDir shared_blood wgcna-signed TRUE >$logDir/pr_shared_wgcna-signed_blood.log | ||
| Rscript compute_pr.R Artery_tibial $datDir/genesets/edges_in_twopathways.txt $plotDir $resultDir shared_artery wgcna-signed TRUE >$logDir/pr_shared_pathways_merged_wgcna-signed_srtery.log | ||
| Rscript compute_pr.R Nerve_tibial $datDir/genesets/edges_in_twopathways.txt $plotDir $resultDir shared_nerve wgcna-signed TRUE >$logDir/pr_shared_pathways_merged_wgcna-signed_nerve.log | ||
| Rscript compute_pr.R Skin $datDir/genesets/edges_in_twopathways.txt $plotDir $resultDir shared_skin wgcna-signed TRUE >$logDir/pr_shared_pathways_merged_wgcna-signed_skin.log | ||
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| Rscript compute_pr.R Subcutaneous $datDir/genesets/edges_in_twopathways.txt $plotDir $resultDir shared_subcutaneous glasso TRUE >$logDir/pr_shared_glasso_subcutaneous.log | ||
| Rscript compute_pr.R Lung $datDir/genesets/edges_in_twopathways.txt $plotDir $resultDir shared_lung glasso TRUE >$logDir/pr_shared_glasso_lung.log | ||
| Rscript compute_pr.R Thyroid $datDir/genesets/edges_in_twopathways.txt $plotDir $resultDir shared_thyroid glasso TRUE >$logDir/pr_shared_glasso_thyroid.log | ||
| Rscript compute_pr.R Muscle $datDir/genesets/edges_in_twopathways.txt $plotDir $resultDir shared_muscle glasso TRUE >$logDir/pr_shared_glasso_muscle.log | ||
| Rscript compute_pr.R Blood $datDir/genesets/edges_in_twopathways.txt $plotDir $resultDir shared_blood glasso TRUE >$logDir/pr_shared_glasso_blood.log | ||
| od.log | ||
| Rscript compute_pr.R Artery_tibial $datDir/genesets/edges_in_twopathways.txt $plotDir $resultDir shared_artery glasso TRUE >$logDir/pr_shared_glasso_srtery.log | ||
| Rscript compute_pr.R Nerve_tibial $datDir/genesets/edges_in_twopathways.txt $plotDir $resultDir shared_nerve glasso TRUE >$logDir/pr_shared_glasso_nerve.log | ||
| Rscript compute_pr.R Skin $datDir/genesets/edges_in_twopathways.txt $plotDir $resultDir shared_skin glasso TRUE >$logDir/pr_shared_glasso_skin.log | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,28 @@ | ||
| #!/bin/sh | ||
| #SBATCH --time=26:0:0 | ||
| #SBATCH --mem=80G | ||
| #SBATCH --partition=shared | ||
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| source ~/.bash_profile | ||
| source /work-zfs/abattle4/parsana/networks_correction/shellscripts/dirconfig | ||
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| cd $scriptDir | ||
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| Rscript compute_pr.R Subcutaneous $datDir/genesets/canonical_pathways_merged.txt $plotDir $resultDir canonical_subcutaneous wgcna-signed FALSE >$logDir/pr_canonical_wgcna-signed_subcutaneous.log | ||
| Rscript compute_pr.R Lung $datDir/genesets/canonical_pathways_merged.txt $plotDir $resultDir canonical_lung wgcna-signed FALSE >$logDir/pr_canonical_wgcna-signed_lung.log | ||
| Rscript compute_pr.R Thyroid $datDir/genesets/canonical_pathways_merged.txt $plotDir $resultDir canonical_thyroid wgcna-signed FALSE >$logDir/pr_canonical_wgcna-signed_thyroid.log | ||
| Rscript compute_pr.R Muscle $datDir/genesets/canonical_pathways_merged.txt $plotDir $resultDir canonical_muscle wgcna-signed FALSE >$logDir/pr_canonical_wgcna-signed_muscle.log | ||
| Rscript compute_pr.R Blood $datDir/genesets/canonical_pathways_merged.txt $plotDir $resultDir canonical_blood wgcna-signed FALSE >$logDir/pr_canonical_wgcna-signed_blood.log | ||
| Rscript compute_pr.R Artery_tibial $datDir/genesets/canonical_pathways_merged.txt $plotDir $resultDir canonical_artery wgcna-signed FALSE >$logDir/pr_canonical_pathways_merged_wgcna-signed_srtery.log | ||
| Rscript compute_pr.R Nerve_tibial $datDir/genesets/canonical_pathways_merged.txt $plotDir $resultDir canonical_nerve wgcna-signed FALSE >$logDir/pr_canonical_pathways_merged_wgcna-signed_nerve.log | ||
| Rscript compute_pr.R Skin $datDir/genesets/canonical_pathways_merged.txt $plotDir $resultDir canonical_skin wgcna-signed FALSE >$logDir/pr_canonical_pathways_merged_wgcna-signed_skin.log | ||
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| Rscript compute_pr.R Subcutaneous $datDir/genesets/tft.txt $plotDir $resultDir tft_subcutaneous wgcna-signed FALSE >$logDir/pr_tft_wgcna-signed_subcutaneous.log | ||
| Rscript compute_pr.R Lung $datDir/genesets/tft.txt $plotDir $resultDir tft_lung wgcna-signed FALSE >$logDir/pr_tft_wgcna-signed_lung.log | ||
| Rscript compute_pr.R Thyroid $datDir/genesets/tft.txt $plotDir $resultDir tft_thyroid wgcna-signed FALSE >$logDir/pr_tft_wgcna-signed_thyroid.log | ||
| Rscript compute_pr.R Muscle $datDir/genesets/tft.txt $plotDir $resultDir tft_muscle wgcna-signed FALSE >$logDir/pr_tft_wgcna-signed_muscle.log | ||
| Rscript compute_pr.R Blood $datDir/genesets/tft.txt $plotDir $resultDir tft_blood wgcna-signed FALSE >$logDir/pr_tft_wgcna-signed_blood.log | ||
| Rscript compute_pr.R Artery_tibial $datDir/genesets/tft.txt $plotDir $resultDir tft_artery wgcna-signed FALSE >$logDir/pr_tft_wgcna-signed_srtery.log | ||
| Rscript compute_pr.R Nerve_tibial $datDir/genesets/tft.txt $plotDir $resultDir tft_nerve wgcna-signed FALSE >$logDir/pr_tft_wgcna-signed_nerve.log | ||
| Rscript compute_pr.R Skin $datDir/genesets/tft.txt $plotDir $resultDir tft_skin wgcna-signed FALSE >$logDir/pr_tft_wgcna-signed_skin.log |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,26 @@ | ||
| #!/bin/sh | ||
| #SBATCH --time=72:0:0 | ||
| #SBATCH --mem=70G | ||
| #SBATCH --partition=shared | ||
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| source ~/.bash_profile | ||
| source /work-zfs/abattle4/parsana/networks_correction/shellscripts/dirconfig | ||
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| cd $scriptDir | ||
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| ## WGCNA networks | ||
| mkdir $networksDir/raw/ | ||
| mkdir $networksDir/rin/ | ||
| mkdir $networksDir/gc/ | ||
| mkdir $networksDir/pc/ | ||
| mkdir $networksDir/halfpc/ | ||
| mkdir $networksDir/quarterpc/ | ||
| Rscript --no-save --no-restore --verbose infer_wgcna.R $datDir/raw_subset.Rdata signed $networksDir/raw/signed_wgcna_networks.Rdata >$logDir/raw_signed_wgcna.log 2>&1 | ||
| Rscript --no-save --no-restore --verbose infer_wgcna.R $datDir/rin_corrected.Rdata signed $networksDir/rin/signed_wgcna_networks.Rdata >$logDir/rin_signed_wgcna.log 2>&1 | ||
| Rscript --no-save --no-restore --verbose infer_wgcna.R $datDir/gc_corrected.Rdata signed $networksDir/gc/signed_wgcna_networks.Rdata >$logDir/gc_signed_wgcna.log 2>&1 | ||
| Rscript --no-save --no-restore --verbose infer_wgcna.R $datDir/exonicRate_corrected.Rdata signed $networksDir/exonicRate/signed_wgcna_networks.Rdata >$logDir/exonicRate_signed_wgcna.log 2>&1 | ||
| Rscript --no-save --no-restore --verbose infer_wgcna.R $datDir/mc_corrected.Rdata signed $networksDir/mc/signed_wgcna_networks.Rdata >$logDir/mc_signed_wgcna.log 2>&1 | ||
| Rscript --no-save --no-restore --verbose infer_wgcna.R $datDir/pc_corrected.Rdata signed $networksDir/pc/signed_wgcna_networks.Rdata >$logDir/pc_signed_wgcna.log 2>&1 | ||
| Rscript --no-save --no-restore --verbose infer_wgcna.R $datDir/halfpc_corrected.Rdata signed $networksDir/halfpc/signed_wgcna_networks.Rdata >$logDir/halfpc_signed_wgcna.log 2>&1 | ||
| Rscript --no-save --no-restore --verbose infer_wgcna.R $datDir/quarterpc_corrected.Rdata signed $networksDir/quarterpc/signed_wgcna_networks.Rdata >$logDir/quarterpc_signed_wgcna.log 2>&1 | ||
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| sbatch --job-name=raw_wgcna_varypower template_power_vary_wgcna.sh raw_subset.Rdata signed raw/power_wgcna_networks.Rdata r2_varypowerraw_wgcna.log | ||
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| sbatch --job-name=rin_wgcna_varypower template_power_vary_wgcna.sh rin_corrected.Rdata signed rin/power_wgcna_networks.Rdata r2_varypowerrin_wgcna.log | ||
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| sbatch --job-name=gc_wgcna_varypower template_power_vary_wgcna.sh gc_corrected.Rdata signed gc/power_wgcna_networks.Rdata r2_varypowergc_wgcna.log | ||
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| sbatch --job-name=mc_wgcna_varypower template_power_vary_wgcna.sh mc_corrected.Rdata signed mc/power_wgcna_networks.Rdata r2_varypowermc_wgcna.log | ||
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| sbatch --job-name=exonicRate_wgcna_varypower template_power_vary_wgcna.sh exonicRate_corrected.Rdata signed exonicRate/power_wgcna_networks.Rdata r2_varypowerexonicRate_wgcna.log | ||
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| sbatch --job-name=pc_wgcna_varypower template_power_vary_wgcna.sh pc_corrected.Rdata signed pc/power_wgcna_networks.Rdata r2_varypowerpc_wgcna.log | ||
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| sbatch --job-name=halfpc_wgcna_varypower template_power_vary_wgcna.sh halfpc_corrected.Rdata signed halfpc/power_wgcna_networks.Rdata r2_varypowerhalfpc_wgcna.log | ||
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| sbatch --job-name=quarterpc_wgcna_varypower template_power_vary_wgcna.sh quarterpc_corrected.Rdata signed quarterpc/power_wgcna_networks.Rdata r2_varypowerquarterpc_wgcna.log | ||
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,13 @@ | ||
| #!/bin/sh | ||
| #SBATCH --time=72:0:0 | ||
| #SBATCH --mem=70G | ||
| #SBATCH --partition=parallel | ||
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| source ~/.bash_profile | ||
| source /work-zfs/abattle4/parsana/networks_correction/shellscripts/dirconfig | ||
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| cd $scriptDir | ||
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| test=$logDir/$4 | ||
| echo $test | ||
| Rscript --no-save --no-restore --verbose infer_wgcna_vary_power.R $datDir/$1 $2 $networksDir/$3 >$logDir/$4 |