运行5_do_MR2.R 报错：Error in file(file, "rt") : 无法打开链结

[xgxofdream]

报错如下：

> setwd(MR_DIR); cat("当前工作目录：", getwd())
当前工作目录： F:/0. MR_Project/03_MR_Basic/AhR(eqtl-a-ENSG00000106546)→DVT(ebi-a-GCST90038615)/5_do_MR> result_file <- file.path(MR_DIR, "MR-Result.csv")
> pFilter <- 1  # 是否根据 P 值过滤？1：不过滤；0.05：过滤
> 
> draw_forest_map <- function(inputFile = null, forestFile = null, forestCol = null) {
+   # 读取输入文件
+   rt <- read.csv(inputFile, header = T, sep = ",", check.names = F)
+   row.names(rt) <- rt$method
+   rt <- rt[rt$pval < pFilter,]
+   method <- rownames(rt)
+   or <- sprintf("%.3f", rt$"or")
+   orLow <- sprintf("%.3f", rt$"or_lci95")
+   orHigh <- sprintf("%.3f", rt$"or_uci95")
+   OR <- paste0(or, "(", orLow, "-", orHigh, ")")
+   pVal <- ifelse(rt$pval < 0.001, "<0.001", sprintf("%.3f", rt$pval))
+ 
+   #输出图形
+   pdf(file = forestFile, width = 7, height = 4.6)
+   n <- nrow(rt)
+   nRow <- n + 1
+   ylim <- c(1, nRow)
+   layout(matrix(c(1, 2), nc = 2), width = c(3.5, 2))
+ 
+   # 左侧
+   xlim <- c(0, 3)
+   par(mar = c(4, 2.5, 2, 1))
+   plot(1, xlim = xlim, ylim = ylim, type = "n", axes = F, xlab = "", ylab = "")
+   text.cex <- 0.8
+   text(0, n:1, method, adj = 0, cex = text.cex)
+   text(1.9, n:1, pVal, adj = 1, cex = text.cex); text(1.9, n + 1, 'pvalue', cex = 1, font = 2, adj = 1)
+   text(3.1, n:1, OR, adj = 1, cex = text.cex); text(2.7, n + 1, 'OR', cex = 1, font = 2, adj = 1)
+ 
+   # 右侧
+   par(mar = c(4, 1, 2, 1), mgp = c(2, 0.5, 0))
+   xlim <- c(min(as.numeric(orLow) * 0.975, as.numeric(orHigh) * 0.975, 0.9), max(as.numeric(orLow), as.numeric(orHigh)) * 1.025)
+   plot(1, xlim = xlim, ylim = ylim, type = "n", axes = F, ylab = "", xaxs = "i", xlab = "OR")
+   arrows(as.numeric(orLow), n:1, as.numeric(orHigh), n:1, angle = 90, code = 3, length = 0.05, col = "darkblue", lwd = 3)
+   abline(v = 1, col = "black", lty = 2, lwd = 2)
+   boxcolor <- ifelse(as.numeric(or) > 1, forestCol, forestCol)
+   points(as.numeric(or), n:1, pch = 15, col = boxcolor, cex = 2)
+   axis(1)
+   dev.off()
+ }
> 
> draw_forest_map(inputFile = result_file, forestFile = "forest_map.pdf", forestCol = "red")
Error in file(file, "rt") : 无法打开链结
Called from: file(file, "rt")