From 5efbc98282e4f58ad4bc1e07adca983310fec116 Mon Sep 17 00:00:00 2001
From: chabrault <37081971+chabrault@users.noreply.github.com>
Date: Thu, 12 Dec 2019 13:41:30 +0100
Subject: [PATCH] Fix bug: add precise QTL peak position in qtl.df

---
 R/qtl.R | 7 ++-----
 1 file changed, 2 insertions(+), 5 deletions(-)

diff --git a/R/qtl.R b/R/qtl.R
index c9292a5..0b24856 100644
--- a/R/qtl.R
+++ b/R/qtl.R
@@ -606,15 +606,11 @@ MIMQTL <- function(cross, numeric.chr.format=FALSE,
   }
   
   QTLest <- temp
-  tmp <- strsplit(QTLest$Terms, split="@")
-  QTLest$linkage.group <- suppressWarnings(as.numeric(unlist(lapply(tmp, `[`, 1))))
-  QTLest$position <- suppressWarnings(as.numeric(unlist(lapply(tmp, `[`, 2))))
   ## Add a column for further order purpose
   QTLest$ord <- seq(from=1, to=nrow(QTLest), by=1)
   if(all(QTLest$df == "NO QTL")){
     QTLest[,c(1:ncol(QTLest))] <- NA
   }
-  
   ## Refine QTL location
   refine <- list()
   if (all(qtl == "NO QTL")) {   # if Null model
@@ -623,6 +619,8 @@ MIMQTL <- function(cross, numeric.chr.format=FALSE,
     refine <- qtl::refineqtl(cross, pheno.col=pheno.col, qtl=qtl,
                              formula=form, method=method, verbose=verbose,
                              keeplodprofile=TRUE)
+    QTLest$position <- refine$pos
+    QTLest$linkage.group <- refine$chr
   }
   
   ## Confidence intervals
@@ -662,7 +660,6 @@ MIMQTL <- function(cross, numeric.chr.format=FALSE,
   CI <- temp4
   CI[,c(2:6)] <- suppressWarnings(lapply(CI[,c(2:6)], as.character))
   CI[,c(2:6)] <- suppressWarnings(lapply(CI[,c(2:6)], as.numeric))
-  CI$position <- round(CI$position, digits=1) # position is rounded in QTLest
   
   ## QTL table
   if(all(apply(QTLest, 1, is.na)) & all(apply(CI[-1], 1, is.na))){