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- library(readr)
- library(dplyr)
- library(cause)
- library(ieugwasr)
- X1=read.table('4_IBS.txt',sep = '\t',header = T)
- X2=read.table('PTSD_2019.txt',sep = '\t',header = T)
- X=gwas_merge(X1,X2,snp_name_cols = c("SNP","SNP"),
- beta_hat_cols = c("b","BETA"),
- se_cols = c("se","SE"),
- A1_cols = c("A1","A1"),
- A2_cols = c("A2","A2"),
- pval_cols = c('p','P')
- )
- set.seed(100)
- varlist <- with(X, sample(snp, size=1000000, replace=FALSE))
- params <- est_cause_params(X, varlist)
- params$rho
- r2_thresh = 0.01
- pval_thresh = 1e-3
- X_clump <- X %>%
- rename(rsid = snp,
- pval = p1) %>%
- ieugwasr::ld_clump(dat = .,
- clump_r2 = r2_thresh,
- clump_p = pval_thresh,
- plink_bin = genetics.binaRies::get_plink_binary(),
- pop = "EUR",
- bfile = './EUR/EUR')
- #windows系统下plink不匹配问题,直接去plink官网下载相应版本放入对应的文件夹中,若出现无法发现目标文件的错误,进入目标文件的文件夹,将文件夹中所有内容均删除之后再尝试
- top_vars <- X_clump$rsid
- res <- cause(X=X, variants = top_vars, param_ests = params)
- res$elpd
- summary(res, ci_size=0.95)$tab
- summary(res)$p
- summary(res)$tab
- plot(res)
- elpd_table <- recompute_elpd_table(res)
- pnorm(res$elpd$z[3])
ld_clump使用本地EUR文档 ,ieugwasr::ld_clump功能
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