Create Combine_outcome_SNP.r

Combine_outcome_SNP.r

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+
+
+library(TwoSampleMR)
+library(dplyr)
+library(googlesheets)
+library(vcfR)
+library(stringr)
+library(mr.raps)
+'%ni%' <- Negate('%in%')
+# ieugwasr::api_status()
+# $`API version`
+# #3.6.7
+# $`Total associations`
+# [1] 126335269652
+# $`Total complete datasets`
+# [1] 34670
+# $`Total public datasets`
+# [1] 34513
+library(MRInstruments)
+library(MVMR)
+library(SNPlocs.Hsapiens.dbSNP144.GRCh37)
+library("SNPlocs.Hsapiens.dbSNP151.GRCh38")
+
+Pathway_SNP="/scratch/ys98038/UKB/plink2_format/COVID_19/Analyses/SNP/"
+Pathway_geno="/scratch/ys98038/UKB/plink2_format/COVID_19/Analyses/Genotype/"
+Pathway_out="/scratch/ys98038/UKB/plink2_format/COVID_19/Analyses/MR_result/result_WBC_01_28_5e-8/"
+
+#load("/scratch/ys98038/UKB/plink2_format/COVID_19/Analyses/SNP/SNPS_37_38.RData")
+
+
+######### Generate outcome dataset using Exposure_SNP_WBC.txt
+for (n in c("HGI_round_4_A2","HGI_round_4_B2","HGI_round_5_A2","HGI_round_5_A2_eur","HGI_round_5_B2","HGI_round_5_B2_eur","HGI_round_5_C2","HGI_round_5_C2_eur")) {
+  exp_dat_file=paste(Pathway_SNP, n, ".txt", sep="")
+  tem_dat <- read.csv(exp_dat_file,header=T, as.is=T,sep = "\t")
+  exp_dat_SNP=read.csv('/scratch/ys98038/UKB/plink2_format/COVID_19/Analyses/SNP/Exposure_SNP_All_trait_01_29.txt',as.is=F,header = F,sep = " ")
+  exp_dat_SNP$V1=as.character.factor(exp_dat_SNP$V1)
+  exp_dat_SNP$V4=as.character.factor(exp_dat_SNP$V4)
+  exp_dat_SNP=exp_dat_SNP[exp_dat_SNP$V5 !="X",]
+  exp_dat_SNP$V5=as.integer(exp_dat_SNP$V5)
+  colnames(tem_dat)[1] <- "CHR"
+  tem_dat$SNP_tem=paste(tem_dat$CHR, tem_dat$POS , sep="_")
+  exp_dat_SNP$SNP_tem=paste(exp_dat_SNP$V5, exp_dat_SNP$V2 , sep="_")
+  tem_dat<-exp_dat_SNP %>% left_join(tem_dat, by= "SNP_tem")
+  Outputfile=paste(Pathway_geno, n, "_All_trait_01_29.txt", sep="")
+  write.table(tem_dat, file= Outputfile, row.names = FALSE, quote = FALSE, col.names = TRUE, sep='\t')
+}