#If TwoSampleMR and MRInstruments packages not installed, run the install.packages and install_github scripts below
# install.packages("devtools")
# library(devtools)
# install_github("MRCIEU/MRInstruments")
# install_github("MRCIEU/TwoSampleMR")

rm(list=ls())
library(TwoSampleMR)
library(MRInstruments)

ao<-available_outcomes()
ao<-ao[ao$subcategory %in% c("Cancer","Cardiovascular"),]
ao<-ao[!duplicated(ao$trait),]
ao<-ao[ao$ncase>500,]
IDs<-ao$id

data(gtex_eqtl)
Pos<-unlist(lapply(c("birc5","survivin"),FUN=function(i)
    grep(i,gtex_eqtl$gene_name,ignore.case=T)))
Birc5<-gtex_eqtl[Pos,]
Birc5<-format_gtex_eqtl(Birc5)

outcome_dat<-extract_outcome_data(
    snps = Birc5$SNP,
    outcomes = IDs
)

dat <- harmonise_data(
    exposure_dat = Birc5, 
    outcome_dat = outcome_dat
)

res<-mr(dat, method_list=c("mr_wald_ratio","mr_ivw"))
res$fdr<-p.adjust(res$pval, method="fdr")
res2<-merge(res,ao[,!names(ao) %in% c("nsnp","path","priority","sd","unit","note","filename","mr","access")],by.x="id.outcome",by.y="id")
res2$OR<-exp(res2$b)
res2$LCI<-exp(res2$b-1.96*res2$se)
res2$UCI<-exp(res2$b+1.96*res2$se)

write.table(res2,"results_update.txt",sep="\t",col.names=T,row.names=F,quote=F)