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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,155 @@ | ||
| #!/usr/bin/env Rscript | ||
| args = commandArgs(trailingOnly = TRUE) | ||
| ########################################################### pop1 ########################################################### | ||
| library(VCM) | ||
| library(XPASS) | ||
| library(mvtnorm) | ||
| library(susieR) | ||
| library(data.table) | ||
| library(RhpcBLASctl) | ||
| set.seed(1) | ||
| blas_set_num_threads(20) | ||
| source("/import/home/share/mingxuan/fine_mapping/utils.R") | ||
| source("/import/home/share/mingxuan/fine_mapping/XMAP.R") | ||
| source("/home/share/mingxuan/taam/code/sldxr.R") | ||
| bim <- fread("/home/share/mingxuan/wegene_qc2/height_ukb_qc2_chr22.bim") | ||
| bp_chr <- bim$V4 | ||
|
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| nrep <- 50 | ||
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| # n1_all <- c(5000, 10000, 15000, 20000) | ||
| n1 <- 15000#as.numeric(args[1]) #10000 | ||
| K_true <- 3#as.numeric(args[2]) #1 | ||
| K <- 5 | ||
|
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| h1_omega <- 0.005 | ||
| h2_omega <- 0.005 | ||
| rho_omega <- 0.8 | ||
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| enrich <- 50 | ||
| rho_sigma <- 0 | ||
|
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| pc_var1 <- 0.05 | ||
| pc_var2 <- 0.2 | ||
|
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| loci <- fread(paste0("/home/share/mingxuan/fine_mapping/loci_chr22_1mb.txt")) | ||
| i_loci <- 29 | ||
| idx_include <- (501:1000) + loci$idx_start[i_loci] - 1 | ||
| p <- length(idx_include) | ||
|
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| bim_loci <- bim[bim$V4 >= loci$left[i_loci] & bim$V4 <= loci$right[i_loci],] | ||
| bp_start <- bim_loci$V4[idx_include[1]] | ||
| bp_end <- bim_loci$V4[idx_include[p]] | ||
| snps <- bim_loci$V2[idx_include] | ||
|
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| R1 <- data.matrix(fread(paste0("/import/home/share/mingxuan/fine_mapping/simulation/data/simu_R1_wg_in_sample_ref_n", n1, "_chr22_loci", i_loci, ".txt"))) | ||
| R1 <- R1[idx_include, idx_include] | ||
| fwrite(R1, file = paste0("/import/home/share/mingxuan/fine_mapping/simulation/susieinf/RunDirectory/R1_ref_n", n1, "_chr22_loci", i_loci, ".ld.gz"), col.names = F, quote = F, sep = "\t") | ||
| Beta1 <- data.matrix(fread(paste0("/import/home/share/mingxuan/fine_mapping/simulation/data/simu_loci_", i_loci, "_small_p", p, "_Beta1_Ktrue", K_true, "_Omega", h1_omega, "_", h2_omega, "_", rho_omega, | ||
| "_enrich", enrich, "_rhoSigma", rho_sigma, "_nrep", nrep, ".txt"))) | ||
|
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||
|
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| for (i in 1:nrep) { | ||
| z_scores1 <- fread(paste0("/import/home/share/mingxuan/fine_mapping/simulation/data/simu_zs1_inflate_pc1_", pc_var1, "_loci_", i_loci, "_small_p", p, "_chr22_n", n1, "_loci", i_loci, "_", "_Ktrue", K_true, "_Omega", h1_omega, "_", h2_omega, "_", rho_omega, | ||
| "_enrich", enrich, "_rhoSigma", rho_sigma, "_nrep", nrep, "_", i, ".txt")) | ||
|
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| zs1 <- z_scores1$V2[loci$idx_left[i_loci]:loci$idx_right[i_loci]][idx_include] | ||
|
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| fwrite(data.frame(Z = zs1), file = paste0("/import/home/share/mingxuan/fine_mapping/simulation/susieinf/RunDirectory/simu_zs1_inflate_susieinf_loci_", i_loci, "_small_p", p, "_chr22_n", n1, "_loci", i_loci, "_", "_Ktrue", K_true, "_Omega", h1_omega, "_", h2_omega, "_", rho_omega, | ||
| "_enrich", enrich, "_rhoSigma", rho_sigma, "_nrep", nrep, "_", i, ".txt")) | ||
|
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||
| susieinf1 <- "python fine-mapping-inf/run_fine_mapping.py --z-col-name Z --save-tsv" | ||
| susieinf1 <- paste0(susieinf1, " --sumstats /import/home/share/mingxuan/fine_mapping/simulation/susieinf/RunDirectory/simu_zs1_inflate_susieinf_loci_", i_loci, "_small_p", p, "_chr22_n", n1, "_loci", i_loci, "_", "_Ktrue", K_true, "_Omega", h1_omega, "_", h2_omega, "_", rho_omega, | ||
| "_enrich", enrich, "_rhoSigma", rho_sigma, "_nrep", nrep, "_", i, ".txt") | ||
| susieinf1 <- paste0(susieinf1, " --num-sparse-effects ", K) | ||
| susieinf1 <- paste0(susieinf1, " --ld-file /import/home/share/mingxuan/fine_mapping/simulation/susieinf/RunDirectory/R1_ref_n", n1, "_chr22_loci", i_loci, ".ld.gz") | ||
| susieinf1 <- paste0(susieinf1, " --n ", n1) | ||
| susieinf1 <- paste0(susieinf1, " --output-prefix /import/home/share/mingxuan/fine_mapping/simulation/susieinf/output/susieinf1_inflate_susieinf_loci_", i_loci, "_small_p", p, "_chr22_n", n1, "_loci", i_loci, "_", "_Ktrue", K_true, "_K",K, "_Omega", h1_omega, "_", h2_omega, "_", rho_omega, | ||
| "_enrich", enrich, "_rhoSigma", rho_sigma, "_nrep", nrep, "_", i) | ||
| system(susieinf1) | ||
|
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||
|
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| cat(i, "-th rep finished.\n") | ||
| } | ||
|
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||
|
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||
|
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||
|
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||
|
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||
| ########################################################### pop1 ########################################################### | ||
| library(VCM) | ||
| library(XPASS) | ||
| library(mvtnorm) | ||
| library(susieR) | ||
| library(data.table) | ||
| library(RhpcBLASctl) | ||
| set.seed(1) | ||
| blas_set_num_threads(20) | ||
| source("/import/home/share/mingxuan/fine_mapping/utils.R") | ||
| source("/import/home/share/mingxuan/fine_mapping/XMAP.R") | ||
| source("/home/share/mingxuan/taam/code/sldxr.R") | ||
| bim <- fread("/home/share/mingxuan/wegene_qc2/height_ukb_qc2_chr22.bim") | ||
| bp_chr <- bim$V4 | ||
|
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| nrep <- 50 | ||
|
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| # n2_all <- c(10000, 15000, 20000) | ||
| n2 <- 20000 | ||
| K_true <- 2#as.numeric(args[2]) #1 | ||
| K <- 5 | ||
|
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||
| h1_omega <- 0.005 | ||
| h2_omega <- 0.005 | ||
| rho_omega <- 0.8 | ||
|
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| enrich <- 50 | ||
| rho_sigma <- 0 | ||
|
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| pc_var1 <- 0.05 | ||
| pc_var2 <- 0.2 | ||
|
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| loci <- fread(paste0("/home/share/mingxuan/fine_mapping/loci_chr22_1mb.txt")) | ||
| i_loci <- 29 | ||
| idx_include <- (501:1000) + loci$idx_start[i_loci] - 1 | ||
| p <- length(idx_include) | ||
|
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| bim_loci <- bim[bim$V4 >= loci$left[i_loci] & bim$V4 <= loci$right[i_loci],] | ||
| bp_start <- bim_loci$V4[idx_include[1]] | ||
| bp_end <- bim_loci$V4[idx_include[p]] | ||
| snps <- bim_loci$V2[idx_include] | ||
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| R2 <- data.matrix(fread(paste0("/import/home/share/mingxuan/fine_mapping/simulation/data/simu_R2_ukb_in_sample_ref_n", n2, "_chr22_loci", i_loci, ".txt"))) | ||
| R2 <- R2[idx_include, idx_include] | ||
| fwrite(R2, file = paste0("/import/home/share/mingxuan/fine_mapping/simulation/susieinf/RunDirectory/R2_ref_n", n2, "_chr22_loci", i_loci, ".ld.gz"), col.names = F, quote = F, sep = "\t") | ||
| Beta2 <- data.matrix(fread(paste0("/import/home/share/mingxuan/fine_mapping/simulation/data/simu_loci_", i_loci, "_small_p", p, "_Beta2_Ktrue", K_true, "_Omega", h1_omega, "_", h2_omega, "_", rho_omega, | ||
| "_enrich", enrich, "_rhoSigma", rho_sigma, "_nrep", nrep, ".txt"))) | ||
|
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| for (i in 1:nrep) { | ||
|
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| z_scores2 <- fread(paste0("/import/home/share/mingxuan/fine_mapping/simulation/data/simu_zs2_inflate_pc1_", pc_var2, "_loci_", i_loci, "_small_p", p, "_chr22_n", n2, "_loci", i_loci, "_", "_Ktrue", K_true, "_Omega", h1_omega, "_", h2_omega, "_", rho_omega, | ||
| "_enrich", enrich, "_rhoSigma", rho_sigma, "_nrep", nrep, "_", i, ".txt")) | ||
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| zs2 <- z_scores2$V2[loci$idx_left[i_loci]:loci$idx_right[i_loci]][idx_include] | ||
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| fwrite(data.frame(Z = zs2), file = paste0("/import/home/share/mingxuan/fine_mapping/simulation/susieinf/RunDirectory/simu_zs2_inflate_susieinf_loci_", i_loci, "_small_p", p, "_chr22_n", n2, "_loci", i_loci, "_", "_Ktrue", K_true, "_Omega", h1_omega, "_", h2_omega, "_", rho_omega, | ||
| "_enrich", enrich, "_rhoSigma", rho_sigma, "_nrep", nrep, "_", i, ".txt")) | ||
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| susieinf2 <- "python fine-mapping-inf/run_fine_mapping.py --z-col-name Z --save-tsv" | ||
| susieinf2 <- paste0(susieinf2, " --sumstats /import/home/share/mingxuan/fine_mapping/simulation/susieinf/RunDirectory/simu_zs2_inflate_susieinf_loci_", i_loci, "_small_p", p, "_chr22_n", n2, "_loci", i_loci, "_", "_Ktrue", K_true, "_Omega", h1_omega, "_", h2_omega, "_", rho_omega, | ||
| "_enrich", enrich, "_rhoSigma", rho_sigma, "_nrep", nrep, "_", i, ".txt") | ||
| susieinf2 <- paste0(susieinf2, " --num-sparse-effects ", K) | ||
| susieinf2 <- paste0(susieinf2, " --ld-file /import/home/share/mingxuan/fine_mapping/simulation/susieinf/RunDirectory/R2_ref_n", n2, "_chr22_loci", i_loci, ".ld.gz") | ||
| susieinf2 <- paste0(susieinf2, " --n ", n2) | ||
| susieinf2 <- paste0(susieinf2, " --output-prefix /import/home/share/mingxuan/fine_mapping/simulation/susieinf/output/susieinf2_inflate_susieinf_loci_", i_loci, "_small_p", p, "_chr22_n", n2, "_loci", i_loci, "_", "_Ktrue", K_true, "_K",K, "_Omega", h1_omega, "_", h2_omega, "_", rho_omega, | ||
| "_enrich", enrich, "_rhoSigma", rho_sigma, "_nrep", nrep, "_", i) | ||
| system(susieinf2) | ||
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| cat(i, "-th rep finished.\n") | ||
| } | ||
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155 changes: 155 additions & 0 deletions
155
results/simulation/simu_susieinf_inflated_small_corrected.R
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,155 @@ | ||
| #!/usr/bin/env Rscript | ||
| args = commandArgs(trailingOnly = TRUE) | ||
| ########################################################### pop1 ########################################################### | ||
| library(VCM) | ||
| library(XPASS) | ||
| library(mvtnorm) | ||
| library(susieR) | ||
| library(data.table) | ||
| library(RhpcBLASctl) | ||
| set.seed(1) | ||
| blas_set_num_threads(15) | ||
| source("/import/home/share/mingxuan/fine_mapping/utils.R") | ||
| source("/import/home/share/mingxuan/fine_mapping/XMAP.R") | ||
| source("/home/share/mingxuan/taam/code/sldxr.R") | ||
| bim <- fread("/home/share/mingxuan/wegene_qc2/height_ukb_qc2_chr22.bim") | ||
| bp_chr <- bim$V4 | ||
|
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||
| nrep <- 50 | ||
|
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| # n1_all <- c(5000, 10000, 15000, 20000) | ||
| n1 <- 10000#as.numeric(args[1]) #10000 | ||
| K_true <- 1#as.numeric(args[2]) #1 | ||
| K <- 5 | ||
|
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| h1_omega <- 0.005 | ||
| h2_omega <- 0.005 | ||
| rho_omega <- 0.8 | ||
|
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| enrich <- 50 | ||
| rho_sigma <- 0 | ||
|
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| pc_var1 <- 0.05 | ||
| pc_var2 <- 0.2 | ||
|
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| loci <- fread(paste0("/home/share/mingxuan/fine_mapping/loci_chr22_1mb.txt")) | ||
| i_loci <- 29 | ||
| idx_include <- (501:1000) + loci$idx_start[i_loci] - 1 | ||
| p <- length(idx_include) | ||
|
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| bim_loci <- bim[bim$V4 >= loci$left[i_loci] & bim$V4 <= loci$right[i_loci],] | ||
| bp_start <- bim_loci$V4[idx_include[1]] | ||
| bp_end <- bim_loci$V4[idx_include[p]] | ||
| snps <- bim_loci$V2[idx_include] | ||
|
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| R1 <- data.matrix(fread(paste0("/import/home/share/mingxuan/fine_mapping/simulation/data/simu_R1_wg_in_sample_ref_n", n1, "_chr22_loci", i_loci, ".txt"))) | ||
| R1 <- R1[idx_include, idx_include] | ||
| fwrite(R1, file = paste0("/import/home/share/mingxuan/fine_mapping/simulation/susieinf/RunDirectory/R1_ref_n", n1, "_chr22_loci", i_loci, ".ld.gz"), col.names = F, quote = F, sep = "\t") | ||
| Beta1 <- data.matrix(fread(paste0("/import/home/share/mingxuan/fine_mapping/simulation/data/simu_loci_", i_loci, "_small_p", p, "_Beta1_Ktrue", K_true, "_Omega", h1_omega, "_", h2_omega, "_", rho_omega, | ||
| "_enrich", enrich, "_rhoSigma", rho_sigma, "_nrep", nrep, ".txt"))) | ||
|
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||
|
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| for (i in 1:nrep) { | ||
| z_scores1 <- fread(paste0("/import/home/share/mingxuan/fine_mapping/simulation/data/simu_zs1_inflate_pc1_", pc_var1, "_corrected_loci_", i_loci, "_small_p", p, "_chr22_n", n1, "_loci", i_loci, "_", "_Ktrue", K_true, "_Omega", h1_omega, "_", h2_omega, "_", rho_omega, | ||
| "_enrich", enrich, "_rhoSigma", rho_sigma, "_nrep", nrep, "_", i, ".txt")) | ||
|
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| zs1 <- z_scores1$V2[loci$idx_left[i_loci]:loci$idx_right[i_loci]][idx_include] | ||
|
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| fwrite(data.frame(Z = zs1), file = paste0("/import/home/share/mingxuan/fine_mapping/simulation/susieinf/RunDirectory/simu_zs1_inflate_susieinf_loci_", i_loci, "_small_p", p, "_chr22_n", n1, "_loci", i_loci, "_", "_Ktrue", K_true, "_Omega", h1_omega, "_", h2_omega, "_", rho_omega, | ||
| "_enrich", enrich, "_rhoSigma", rho_sigma, "_nrep", nrep, "_", i, ".txt")) | ||
|
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| susieinf1 <- "python fine-mapping-inf/run_fine_mapping.py --z-col-name Z --save-tsv" | ||
| susieinf1 <- paste0(susieinf1, " --sumstats /import/home/share/mingxuan/fine_mapping/simulation/susieinf/RunDirectory/simu_zs1_inflate_susieinf_loci_", i_loci, "_small_p", p, "_chr22_n", n1, "_loci", i_loci, "_", "_Ktrue", K_true, "_Omega", h1_omega, "_", h2_omega, "_", rho_omega, | ||
| "_enrich", enrich, "_rhoSigma", rho_sigma, "_nrep", nrep, "_", i, ".txt") | ||
| susieinf1 <- paste0(susieinf1, " --num-sparse-effects ", K) | ||
| susieinf1 <- paste0(susieinf1, " --ld-file /import/home/share/mingxuan/fine_mapping/simulation/susieinf/RunDirectory/R1_ref_n", n1, "_chr22_loci", i_loci, ".ld.gz") | ||
| susieinf1 <- paste0(susieinf1, " --n ", n1) | ||
| susieinf1 <- paste0(susieinf1, " --output-prefix /import/home/share/mingxuan/fine_mapping/simulation/susieinf/output/susieinf1_inflate_susieinf_loci_", i_loci, "_small_p", p, "_chr22_n", n1, "_corrected_loci", i_loci, "_", "_Ktrue", K_true, "_K",K, "_Omega", h1_omega, "_", h2_omega, "_", rho_omega, | ||
| "_enrich", enrich, "_rhoSigma", rho_sigma, "_nrep", nrep, "_", i) | ||
| system(susieinf1) | ||
|
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|
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| cat(i, "-th rep finished.\n") | ||
| } | ||
|
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|
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|
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| ########################################################### pop1 ########################################################### | ||
| library(VCM) | ||
| library(XPASS) | ||
| library(mvtnorm) | ||
| library(susieR) | ||
| library(data.table) | ||
| library(RhpcBLASctl) | ||
| set.seed(1) | ||
| blas_set_num_threads(20) | ||
| source("/import/home/share/mingxuan/fine_mapping/utils.R") | ||
| source("/import/home/share/mingxuan/fine_mapping/XMAP.R") | ||
| source("/home/share/mingxuan/taam/code/sldxr.R") | ||
| bim <- fread("/home/share/mingxuan/wegene_qc2/height_ukb_qc2_chr22.bim") | ||
| bp_chr <- bim$V4 | ||
|
|
||
| nrep <- 50 | ||
|
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||
| # n2_all <- c(10000, 15000, 20000) | ||
| n2 <- 20000 | ||
| K_true <- 1#as.numeric(args[2]) #1 | ||
| K <- 5 | ||
|
|
||
| h1_omega <- 0.005 | ||
| h2_omega <- 0.005 | ||
| rho_omega <- 0.8 | ||
|
|
||
| enrich <- 50 | ||
| rho_sigma <- 0 | ||
|
|
||
| pc_var1 <- 0.05 | ||
| pc_var2 <- 0.2 | ||
|
|
||
| loci <- fread(paste0("/home/share/mingxuan/fine_mapping/loci_chr22_1mb.txt")) | ||
| i_loci <- 29 | ||
| idx_include <- (501:1000) + loci$idx_start[i_loci] - 1 | ||
| p <- length(idx_include) | ||
|
|
||
| bim_loci <- bim[bim$V4 >= loci$left[i_loci] & bim$V4 <= loci$right[i_loci],] | ||
| bp_start <- bim_loci$V4[idx_include[1]] | ||
| bp_end <- bim_loci$V4[idx_include[p]] | ||
| snps <- bim_loci$V2[idx_include] | ||
|
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||
|
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||
|
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| R2 <- data.matrix(fread(paste0("/import/home/share/mingxuan/fine_mapping/simulation/data/simu_R2_ukb_in_sample_ref_n", n2, "_chr22_loci", i_loci, ".txt"))) | ||
| R2 <- R2[idx_include, idx_include] | ||
| fwrite(R2, file = paste0("/import/home/share/mingxuan/fine_mapping/simulation/susieinf/RunDirectory/R2_ref_n", n2, "_chr22_loci", i_loci, ".ld.gz"), col.names = F, quote = F, sep = "\t") | ||
| Beta2 <- data.matrix(fread(paste0("/import/home/share/mingxuan/fine_mapping/simulation/data/simu_loci_", i_loci, "_small_p", p, "_Beta2_Ktrue", K_true, "_Omega", h1_omega, "_", h2_omega, "_", rho_omega, | ||
| "_enrich", enrich, "_rhoSigma", rho_sigma, "_nrep", nrep, ".txt"))) | ||
|
|
||
| for (i in 1:nrep) { | ||
|
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||
| z_scores2 <- fread(paste0("/import/home/share/mingxuan/fine_mapping/simulation/data/simu_zs2_inflate_pc1_", pc_var2, "_corrected_loci_", i_loci, "_small_p", p, "_chr22_n", n2, "_loci", i_loci, "_", "_Ktrue", K_true, "_Omega", h1_omega, "_", h2_omega, "_", rho_omega, | ||
| "_enrich", enrich, "_rhoSigma", rho_sigma, "_nrep", nrep, "_", i, ".txt")) | ||
|
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||
| zs2 <- z_scores2$V2[loci$idx_left[i_loci]:loci$idx_right[i_loci]][idx_include] | ||
|
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||
|
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| fwrite(data.frame(Z = zs2), file = paste0("/import/home/share/mingxuan/fine_mapping/simulation/susieinf/RunDirectory/simu_zs2_inflate_susieinf_loci_", i_loci, "_small_p", p, "_chr22_n", n2, "_loci", i_loci, "_", "_Ktrue", K_true, "_Omega", h1_omega, "_", h2_omega, "_", rho_omega, | ||
| "_enrich", enrich, "_rhoSigma", rho_sigma, "_nrep", nrep, "_", i, ".txt")) | ||
|
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||
|
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| susieinf2 <- "python fine-mapping-inf/run_fine_mapping.py --z-col-name Z --save-tsv" | ||
| susieinf2 <- paste0(susieinf2, " --sumstats /import/home/share/mingxuan/fine_mapping/simulation/susieinf/RunDirectory/simu_zs2_inflate_susieinf_loci_", i_loci, "_small_p", p, "_chr22_n", n2, "_loci", i_loci, "_", "_Ktrue", K_true, "_Omega", h1_omega, "_", h2_omega, "_", rho_omega, | ||
| "_enrich", enrich, "_rhoSigma", rho_sigma, "_nrep", nrep, "_", i, ".txt") | ||
| susieinf2 <- paste0(susieinf2, " --num-sparse-effects ", K) | ||
| susieinf2 <- paste0(susieinf2, " --ld-file /import/home/share/mingxuan/fine_mapping/simulation/susieinf/RunDirectory/R2_ref_n", n2, "_chr22_loci", i_loci, ".ld.gz") | ||
| susieinf2 <- paste0(susieinf2, " --n ", n2) | ||
| susieinf2 <- paste0(susieinf2, " --output-prefix /import/home/share/mingxuan/fine_mapping/simulation/susieinf/output/susieinf2_inflate_susieinf_loci_", i_loci, "_small_p", p, "_chr22_n", n2, "_corrected_loci", i_loci, "_", "_Ktrue", K_true, "_K",K, "_Omega", h1_omega, "_", h2_omega, "_", rho_omega, | ||
| "_enrich", enrich, "_rhoSigma", rho_sigma, "_nrep", nrep, "_", i) | ||
| system(susieinf2) | ||
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| cat(i, "-th rep finished.\n") | ||
| } | ||
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