孟德尔随机分析求助
各位大神,做TSMR遇到困难,通过read_outcome_data处理outcome是报错如下,请问哪位老师有相关的经验吗?代码如下,不甚感激~
提取暴露SNP
> library(TwoSampleMR)
> exposure<-read.csv(file.choose("exposure_ECD.csv"),header=T)
> exp_clumped<-clump_data(exposure,clump_kb = 10000,clump_r2 = 0.1,clump_p1 = 1,clump_p2 = 1,pop = "EUR")
提取结局SNP
> setwd("D:/!孟德尔随机研究/ECD and CKD/数据处理")
> c<-read.table(file.choose("CKD_EUR_JW_20180223_nstud23.dbgap.txt"),header=T)
> d<-merge(exp_clumped,c,by.x = "SNP",by.y = "RSID")
> write.csv(d,file = "outcome.csv")
> outcome_dat<-read_outcome_data(snps = exp_clumped$SNP,filename = "outcome.csv",sep = ",",snp_col = "SNP",beta_col = "beta",se_col = "se",eaf_col = "eaf",effect_allele_col = "effect_allele",other_allele_col = "other_allele",pval_col = "p")
(问题所在)Error in data.table::fread(filename, header = TRUE, sep = sep) : 文件'outcome.csv' 不存在, 或不可读. getwd()=='D:/!孟德尔随机研究/NAFLD and CKD/数据处理'
最后编辑于 2023-09-22 · 浏览 613