GWAS_or <- read.csv('C:\\Users\\user\\Documents\\Studie\\PhD\\Gen analyse\\GWAS\\gwas-association-downloaded_2019-11-14-EFO_0000249_AD.tsv', sep = '\t', header = T)
Trans_eQTL <- read.csv('C:\\Users\\user\\Documents\\Studie\\PhD\\Gen analyse\\eQTL\\trans-eQTL_significant_20181017.txt.gz', sep = '\t', header = T)
Cis_eQTL <- read.csv('C:\\Users\\user\\Documents\\Studie\\PhD\\Gen analyse\\eQTL\\cis-eQTL_significant_20181017.txt.gz', sep = '\t', header = T)
Trait <- c("Alzheimer's disease")

GWAS_T <- data.frame()
GWAS_SP <- data.frame()
GWAS_Uni <- data.frame()
GWAS_T <- GWAS_or[+which(GWAS_or$DISEASE.TRAIT %in% Trait), ]
GWAS_SP <- separate_rows(GWAS_T, SNPS, sep = ";\\s+")
GWAS_Uni <- GWAS_SP[!duplicated(GWAS_SP$SNPS),]

eQTL_analysed_file <- data.frame(SNPs = as.character(GWAS_Uni$SNPS),
                                 Trans = character(length = length(GWAS_Uni$SNPS)),
                                 Cis = character(length = length(GWAS_Uni$SNPS)),
                                 GWAS = as.character(GWAS_Uni$MAPPED_GENE))


TransinGWAS <-  subset(Trans_eQTL, SNP %in% GWAS_Uni$SNPS)
CisinGWAS <- subset(Cis_eQTL, SNP %in% GWAS_Uni$SNPS)



for(i in eQTL_analysed_file$SNPs){

  eQTL_analysed_file$Trans[i] <- ifelse(i %in% Trans_eQTL$SNP == TRUE,
                                        (c(as.character(Trans_eQTL$GeneSymbol[Trans_eQTL$SNP == as.character(i)]))),
                                        NA)
  eQTL_analysed_file$Cis[i] <- ifelse(i%in% Cis_eQTL$SNP == TRUE,
                                     (c(as.character(Cis_eQTL$GeneSymbol[Cis_eQTL$SNP== as.character(i)]))),
                                     NA)
}