cross disorder revision #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
#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
#generate union gene list