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| #H-MAGMA results are stored: /proj/hyejunglab/crossdisorder/MAGMA/result_harper/magma1.07/adult_brain/ab_results | ||
| #SCZ: scz.clozuk.2017_AB_wointron.genes.genes.out | ||
| #ASD: asd.daly.2017_AB_wointron.genes.genes.out | ||
| #BD: bp.pgc.2018_AB_wointron.genes.genes.out | ||
| #Coloc for SCZ: /proj/hyejunglab/disorder/Schizophrenia_clozuk/capstone4/coloc_outputfile_SCZ_Capstone4_cisQTL.rda | ||
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| #TWAS results are stored: /proj/hyejunglab/expression/capstone1_disorder | ||
| #SCZ: SCZ_TWAS.csv | ||
| #ASD: ASD_TWAS.csv | ||
| #BD: BD_TWAS.csv | ||
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| #protein-coding genes can be obtained by: /proj/hyejunglab/chr/geneAnno_allgenes.rda | ||
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| #TWAS comparison | ||
| #1. Read H-MAGMA SCZ results | ||
| #2. Read TWAS SCZ results | ||
| #3. Select H-MAGMA genes that were detected in TWAS SCZ results | ||
| #4. Calculate FDR from the H-MAGMA | ||
| #5. Take FDR<0.05 genes from H-MAGMA | ||
| #6. Calculate TWAS FDR from TWAS.P | ||
| #7. Take FDR<0.05 genes from TWAS | ||
| #8. Make a Venn diagram with H-MAGMA genes vs. TWAS genes | ||
| #9. Run Fisher’s exact test (edited) | ||
| #Repeat this for ASD and BD | ||
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| module add r/3.5.2 | ||
| R CMD BATCH --no-save /nas/longleaf/home/hubenxia/project/cross/rda2txt.R | ||
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| cd /proj/hyejunglab/crossdisorder/MAGMA/result_harper/magma1.07/adult_brain/ab_results | ||
| SCZ=scz.clozuk.2017_AB_wointron.genes.genes.out | ||
| ASD=asd.daly.2017_AB_wointron.genes.genes.out | ||
| BD=bp.pgc.2018_AB_wointron.genes.genes.out | ||
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| SCZ_TWAS=/proj/hyejunglab/expression/capstone1_disorder/SCZ_TWAS.csv | ||
| ASD_TWAS=/proj/hyejunglab/expression/capstone1_disorder/ASD_TWAS.csv | ||
| BD_TWAS=/proj/hyejunglab/expression/capstone1_disorder/BD_TWAS.csv | ||
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| MAGMAv26_SCZ=/proj/hyejunglab/crossdisorder/MAGMA/result_harper/magma1.07/new_default/scz.clozuk.2017_MAGMA.genes.out | ||
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| dos2unix /nas/longleaf/home/hubenxia/project/cross/selection2.py | ||
| python /nas/longleaf/home/hubenxia/project/cross/selection2.py -t $SCZ_TWAS -d $SCZ -o /proj/hyejunglab/crossdisorder/Revision/hubenxia/twas_SCZ_gene.txt -k /proj/hyejunglab/crossdisorder/Revision/hubenxia/twas_SCZ_overlap_gene.txt | ||
| python /nas/longleaf/home/hubenxia/project/cross/selection2.py -t $ASD_TWAS -d $ASD -o /proj/hyejunglab/crossdisorder/Revision/hubenxia/twas_ASD_gene.txt -k /proj/hyejunglab/crossdisorder/Revision/hubenxia/twas_ASD_overlap_gene.txt | ||
| python /nas/longleaf/home/hubenxia/project/cross/selection2.py -t $BD_TWAS -d $BD -o /proj/hyejunglab/crossdisorder/Revision/hubenxia/twas_BD_gene.txt -k /proj/hyejunglab/crossdisorder/Revision/hubenxia/twas_BD_overlap_gene.txt | ||
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| python /nas/longleaf/home/hubenxia/project/cross/selection2.py -t $SCZ_TWAS -d ${MAGMAv26_SCZ} -o /proj/hyejunglab/crossdisorder/Revision/hubenxia/twas_SCZ_gene.txt -k /proj/hyejunglab/crossdisorder/Revision/hubenxia/twas_MAGMAv26_SCZ_overlap_gene.txt | ||
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| module add r/3.5.2 | ||
| R CMD BATCH --no-save /nas/longleaf/home/hubenxia/project/cross/venn2.R | ||
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| #Coloc comparison | ||
| #1. Load coloc results | ||
| #2. Take genes from coloc_result_sig$locus2gene: you should get ENSG IDs (remove .) | ||
| #3. Load eQTL source file: load("/proj/hyejunglab/eQTL/capstone4/eQTL/adultonly/eQTL_GRanges_colocinput.rda") | ||
| #4. Retrieve genes from qtlranges: qtlranges$gene -> remove . & unique -> this will be your background gene list | ||
| #5. Read H-MAGMA SCZ results | ||
| #6. Select H-MAGMA genes that were detected in background genes. | ||
| #7. Take FDR<0.05 genes from H-MAGMA | ||
| #8. Compare H-MAGMA genes from coloc genes from (2) | ||
| #9. Make a Venn diagram with H-MAGMA genes vs. coloc genes | ||
| #10. Run Fisher’s exact test | ||
| #Save all files in this revision directory: /proj/hyejunglab/crossdisorder/Revision | ||
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| module add r/3.5.2 | ||
| R CMD BATCH --no-save /nas/longleaf/home/hubenxia/project/cross/rda2txt.R | ||
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| cd /proj/hyejunglab/crossdisorder/MAGMA/result_harper/magma1.07/adult_brain/ab_results | ||
| SCZ=scz.clozuk.2017_AB_wointron.genes.genes.out | ||
| MAGMAv26_SCZ=/proj/hyejunglab/crossdisorder/MAGMA/result_harper/magma1.07/new_default/scz.clozuk.2017_MAGMA.genes.out | ||
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| background=/proj/hyejunglab/crossdisorder/Revision/hubenxia/coloc_background.txt | ||
| coloc=/proj/hyejunglab/crossdisorder/Revision/hubenxia/coloc.txt | ||
| dos2unix /nas/longleaf/home/hubenxia/project/cross/selection.py | ||
| python /nas/longleaf/home/hubenxia/project/cross/selection.py -b $background -d $SCZ -c $coloc -o /proj/hyejunglab/crossdisorder/Revision/hubenxia/background_SCZ.txt -k /proj/hyejunglab/crossdisorder/Revision/hubenxia/coloc_backgroundid.txt -e /proj/hyejunglab/crossdisorder/Revision/hubenxia/SCZ_gene.txt | ||
| python /nas/longleaf/home/hubenxia/project/cross/selection.py -b $background -d ${MAGMAv26_SCZ} -c $coloc -o /proj/hyejunglab/crossdisorder/Revision/hubenxia/background_SCZ.txt -k /proj/hyejunglab/crossdisorder/Revision/hubenxia/coloc_backgroundid.txt -e /proj/hyejunglab/crossdisorder/Revision/hubenxia/MAGMAv26_SCZ_gene.txt | ||
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| module add r/3.5.2 | ||
| R CMD BATCH --no-save /nas/longleaf/home/hubenxia/project/cross/venn.R | ||
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| ASD_BD=/proj/hyejunglab/crossdisorder/MAGMA/RRHO/RRHO_GO_MostUpregulatedASD_VS_Bipolar.csv | ||
| ASD_SCZ=/proj/hyejunglab/crossdisorder/MAGMA/RRHO/RRHO_GO_MostUpregulatedASD_VS_Schizophrenia.csv | ||
| ASD_MDD=/proj/hyejunglab/crossdisorder/MAGMA/RRHO/RRHO_GO_MostUpregulatedASD_VS_MDD.csv | ||
| ASD_ADHD=/proj/hyejunglab/crossdisorder/MAGMA/RRHO/RRHO_GO_MostUpregulatedADHD_VS_ASD.csv | ||
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| ASD=($ASD_SCZ $ASD_MDD $ASD_ADHD) | ||
| ASD_name=("ASD_SCZ" "ASD_MDD" "ASD_ADHD") | ||
| for i in {0..2} | ||
| do | ||
| filename=ASD_BD_"${ASD_name[i]}".txt | ||
| dos2unix /nas/longleaf/home/hubenxia/project/cross/selection3.py | ||
| python /nas/longleaf/home/hubenxia/project/cross/selection3.py -a $ASD_BD -c ASD_BD -b "${ASD[i]}" -d "${ASD_name[i]}" -o /proj/hyejunglab/crossdisorder/Revision/hubenxia/$filename | ||
| done | ||
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| ASD_BD_ASD_ADHD=/proj/hyejunglab/crossdisorder/Revision/hubenxia/ASD_BD_ASD_ADHD.txt | ||
| ASD_BD_ASD_MDD=/proj/hyejunglab/crossdisorder/Revision/hubenxia/ASD_BD_ASD_MDD.txt | ||
| ASD_BD_ASD_SCZ=/proj/hyejunglab/crossdisorder/Revision/hubenxia/ASD_BD_ASD_SCZ.txt | ||
| ASD=($ASD_BD_ASD_ADHD $ASD_BD_ASD_MDD $ASD_BD_ASD_SCZ) | ||
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| for i in {0..2} | ||
| do | ||
| cat "${ASD[i]}" >> /proj/hyejunglab/crossdisorder/Revision/hubenxia/ASD_BD_merge.txt | ||
| filename=ASD_BD_class_temp.txt | ||
| cat "${ASD[i]}" | awk '{print $1}' >> /proj/hyejunglab/crossdisorder/Revision/hubenxia/$filename | ||
| done | ||
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| cat /proj/hyejunglab/crossdisorder/Revision/hubenxia/$filename | sort | uniq > /proj/hyejunglab/crossdisorder/Revision/hubenxia/ASD_BD_class.txt | ||
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| dos2unix /nas/longleaf/home/hubenxia/project/cross/selection4.py | ||
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| input=/proj/hyejunglab/crossdisorder/Revision/hubenxia/ASD_BD_class.txt | ||
| target=/proj/hyejunglab/crossdisorder/Revision/hubenxia/ASD_BD_merge.txt | ||
| python /nas/longleaf/home/hubenxia/project/cross/selection4.py -a $input -b $target -o /proj/hyejunglab/crossdisorder/Revision/hubenxia/ASD_union.txt | ||
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| ADHD_BD=/proj/hyejunglab/crossdisorder/MAGMA/RRHO/RRHO_GO_MostUpregulatedADHD_VS_Bipolar.csv | ||
| ADHD_SCZ=/proj/hyejunglab/crossdisorder/MAGMA/RRHO/RRHO_GO_MostUpregulatedADHD_VS_Schizophrenia.csv | ||
| ADHD_MDD=/proj/hyejunglab/crossdisorder/MAGMA/RRHO/RRHO_GO_MostUpregulatedADHD_VS_MDD.csv | ||
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| ADHD=($ADHD_SCZ $ADHD_MDD) | ||
| ADHD_name=("ADHD_SCZ" "ADHD_MDD") | ||
| for i in {0..1} | ||
| do | ||
| filename=ADHD_BD_"${ADHD_name[i]}".txt | ||
| dos2unix /nas/longleaf/home/hubenxia/project/cross/selection3.py | ||
| python /nas/longleaf/home/hubenxia/project/cross/selection3.py -a $ADHD_BD -c ADHD_BD -b "${ADHD[i]}" -d "${ADHD_name[i]}" -o /proj/hyejunglab/crossdisorder/Revision/hubenxia/$filename | ||
| done | ||
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| ADHD_BD_ADHD_MDD=/proj/hyejunglab/crossdisorder/Revision/hubenxia/ADHD_BD_ADHD_MDD.txt | ||
| ADHD_BD_ADHD_SCZ=/proj/hyejunglab/crossdisorder/Revision/hubenxia/ADHD_BD_ADHD_SCZ.txt | ||
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| ADHD=($ADHD_BD_ADHD_MDD $ADHD_BD_ADHD_SCZ) | ||
| for i in {0..1} | ||
| do | ||
| cat "${ADHD[i]}" >> /proj/hyejunglab/crossdisorder/Revision/hubenxia/ADHD_BD_merge.txt | ||
| #filename=ADHD_BD_class_temp.txt | ||
| #cat "${ADHD[i]}" | awk '{print $1}' >> /proj/hyejunglab/crossdisorder/Revision/hubenxia/$filename | ||
| done | ||
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| cat /proj/hyejunglab/crossdisorder/Revision/hubenxia/$filename | sort | uniq > /proj/hyejunglab/crossdisorder/Revision/hubenxia/ADHD_BD_class.txt | ||
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| dos2unix /nas/longleaf/home/hubenxia/project/cross/selection5.py | ||
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| input=/proj/hyejunglab/crossdisorder/Revision/hubenxia/ADHD_BD_class.txt | ||
| target=/proj/hyejunglab/crossdisorder/Revision/hubenxia/ADHD_BD_merge.txt | ||
| python /nas/longleaf/home/hubenxia/project/cross/selection5.py -a $input -b $target -o /proj/hyejunglab/crossdisorder/Revision/hubenxia/ADHD_union.txt | ||
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| BD_SCZ=/proj/hyejunglab/crossdisorder/MAGMA/RRHO/RRHO_GO_MostUpregulatedBipolar_VS_Schizophrenia.csv | ||
| BD_MDD=/proj/hyejunglab/crossdisorder/MAGMA/RRHO/RRHO_GO_MostUpregulatedBipolar_VS_MDD.csv | ||
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| BD=($BD_MDD) | ||
| BD_name=("BD_MDD") | ||
| for i in 0 | ||
| do | ||
| filename=BD_SCZ_"${BD_name[i]}".txt | ||
| dos2unix /nas/longleaf/home/hubenxia/project/cross/selection3.py | ||
| python /nas/longleaf/home/hubenxia/project/cross/selection3.py -a $BD_SCZ -c BD_SCZ -b "${BD[i]}" -d "${BD_name[i]}" -o /proj/hyejunglab/crossdisorder/Revision/hubenxia/$filename | ||
| done | ||
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| input=/proj/hyejunglab/crossdisorder/Revision/hubenxia/BD_SCZ_BD_MDD.txt | ||
| cat $input | awk -v OFS="\t" '{print $1,"BD","MDD","SCZ"}' > /proj/hyejunglab/crossdisorder/Revision/hubenxia/BD_union.txt | ||
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| SCZ_MDD=/proj/hyejunglab/crossdisorder/MAGMA/RRHO/RRHO_GO_MostUpregulatedSchizophrenia_VS_MDD.csv | ||
| cat $SCZ_MDD | awk -v OFS="\t" 'BEGIN {print "geneid","SCZ","MDD"} {print $0,"SCZ","MDD"}' > /proj/hyejunglab/crossdisorder/Revision/hubenxia/SCZ_union.txt | ||
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| cd /proj/hyejunglab/crossdisorder/Revision/hubenxia/ | ||
| dos2unix /nas/longleaf/home/hubenxia/project/cross/concate.py | ||
| python /nas/longleaf/home/hubenxia/project/cross/concate.py -a ASD_union.txt -b BD_union.txt -c ADHD_union.txt -o all_union.txt | ||
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This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,7 @@ | ||
| load("/proj/hyejunglab/disorder/Schizophrenia_clozuk/capstone4/coloc_outputfile_SCZ_Capstone4_cisQTL.rda") | ||
| write.table(coloc_result_sig$locus2gene,file="/proj/hyejunglab/crossdisorder/Revision/hubenxia/coloc.txt",sep="\t",quote=F,row.names=F) | ||
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| load("/proj/hyejunglab/eQTL/capstone4/eQTL/adultonly/eQTL_GRanges_colocinput.rda") | ||
| write.table(qtlranges$gene,file="/proj/hyejunglab/crossdisorder/Revision/hubenxia/coloc_background.txt",sep="\t",quote=F,row.names=F) | ||
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| load("/proj/hyejunglab/crossdisorder/MAGMA/result_harper/magma1.07/fetal_brain/GO_FB/pval_0.05/GO_GSEA_protein-coding_genes_MHCextrm_BD.PGC.2019_FB.rda") |