The codes and results repository for the MR analyses to understand the effect of alternative splicing on COVID-19.
under scripts
01.makeoutcome.rds.R: scripts to format outcome GWAS dataset to run MR.02.makeexposure_sQTL_EUR.R: scripts to format exposure GWAS dataset to run MR.03.MRsQTL_EUR.R: scripts to run MR using sQTL dataset as exposure.04.MRsQTL_summarise.R: scripts to summarise MR results using sQTL dataset.05.Fig3.MR.R: scripts to make Fig 3 (forrest plot).06.B1_MR.R: scripts to run MR for B1 phenotype.07.coloc.lung.R&08.coloc.wbc.R: scripts to run colocalization analysis using sQTL dataset.09.MRsQTL_coloc_sensitivity.R: scripts to format colocalization analysis results.10.MReQTL_EUR.R: scripts to run MR using eQTL dataset as exposure.11.coloc.wbc.eQTL.R&12.coloc.lung.eQTL.R: scripts to run colocalization analysis using eQTL dataset.13.MReQTL_sensitivity.R: scripts to summarise MR results using eQTL dataset.14.HPA.scRNAseq.heatmap.R: scripts to make Fig. 4A and 4B.15.scRNAseq_covid.R: scripts to make Fig. 4C.16.coloc_otherdiseases.R: scripts to run colocalization for other diseases than COVID-19.
under scripts/violin_sashimi_work
Codes to generate Fig 2 (violin plot) and Supplementary Fig 1 (sashimi plot) were stored. For details, please refer to the Readme file within the folder.