#Use coloc::coloc.abf for colocalization
qtl_file = ""
gwas_file = ""
qtl <- data.table::fread(qtl_file, sep="auto", header = T)
gwas <- data.table::fread(gwas_file, sep="auto", header = T)

dup <- duplicated(qtl$SNP)
if(any(dup)){
  qtl <- qtl[!dup,]
}
dup <- duplicated(gwas$SNP)
if(any(dup)){
  gwas <- gwas[!dup,]
}
if(is.character(qtl$pval)){
  qtl$pval <- gsub("e", "E", qtl$pval)
  qtl$pval <- as.numeric(qtl$pval)
}
if(is.character(gwas$pval)){
  gwas$pval <- gsub("e", "E", gwas$pval)
  gwas$pval <- as.numeric(gwas$pval)
}
qtl <- subset(qtl, pval > 0)
gwas <- subset(gwas, pval > 0)
commonsnps <- qtl$SNP[qtl$SNP %in% gwas$SNP]
qtl <- qtl[qtl$SNP %in% commonsnps, ] %>% dplyr::arrange(SNP)
gwas <- gwas[gwas$SNP %in% commonsnps, ] %>% dplyr::arrange(SNP)

input <- merge(qtl, gwas, by="SNP", all=FALSE, suffixes=c("_1","_2"), sort=F)

type1 <- "quant"

if(!all(is.na(qtl$type))){
  type1 <- qtl$type[1]
}
if(!is.null(qtl_type)){
  type1 <- qtl_type
}

type2 <- "cc"

if(!all(is.na(gwas$type))){
  type2 <- gwas$type[1]
}
if(!is.null(gwas_type)){
  type2 <- gwas_type
}

if(is.null(qtl_S)){
  qtl_S <- qtl$s
}
if(is.null(gwas_S)){
  gwas_S <- gwas$s
}
if("N" %in% colnames(qtl) && !all(is.na(qtl$N))){
  qtl_samplesize <- qtl$N[1]
}
if(type1 == "cc"){
  dataset1 <- list(pvalues=input$pval_1,
                    type=type1, s=qtl_S[1],
                    N=qtl_samplesize, MAF=input$maf_1,
                    snp=input$SNP)
}else{
  dataset1 <- list(pvalues=input$pval_1,
                    type=type1, N=qtl_samplesize, MAF=input$maf_1, snp=input$SNP)#qtl Y轴
}

if(type2 == "cc"){
  dataset2 <- list(pvalues=input$pval_2, type=type2,
                    s=gwas_S[1], N=gwas_samplesize,MAF=input$maf_2,
                    snp=input$SNP)
}else{
  dataset2 <- list(pvalues=input$pval_2, type=type2, N=gwas_samplesize,
                    MAF=input$maf_2, snp=input$SNP)
}
if("position" %in% names(dataset1) && "position" %in% names(dataset2)){
  dataset2$position <- dataset1$position
}
file_aa = paste0(get_basename(qtl_file), "_", get_basename(gwas_file))

coloc_res <- coloc::coloc.abf(dataset1,
                               dataset2)
if(is.null(to_dir)){
  time_str <- format(Sys.time(), "%Y%m%d%H%M%S")
  to_dir <- paste(time_str, "for_coloc_res", sep="_")
}
to_dir<-check_dir(to_dir)
coloc_res_name <- paste0(to_dir, "/coloc_res_", file_aa, ".csv")

a = as.data.frame(coloc_res$summary)
data.table::fwrite(a, coloc_res_name, row.names = T, col.names = T)

coloc_snp_results <- paste0(to_dir, "/coloc_data_", file_aa, ".csv")

data.table::fwrite(coloc_res$results, coloc_snp_results, row.names = T, col.names = T)