From 44a3f49618e7ab62f15c95231f1f94cdb2819e0d Mon Sep 17 00:00:00 2001
From: chabrault <37081971+chabrault@users.noreply.github.com>
Date: Wed, 11 Dec 2019 11:09:59 +0100
Subject: [PATCH] Fix minor bug in MIMQTL

Problem when position of marker is too precise: position in QTLest is rounded with 1 digit whereas position in CI is not rounded. This caused a problem when merging these data frames.
---
 R/qtl.R | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/R/qtl.R b/R/qtl.R
index b4f0eec..c9292a5 100644
--- a/R/qtl.R
+++ b/R/qtl.R
@@ -662,6 +662,7 @@ 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))){
@@ -670,7 +671,7 @@ MIMQTL <- function(cross, numeric.chr.format=FALSE,
                          "est.BC"=NA, "est.AD"=NA, "est.BD"=NA,
                          "effect.Af"=NA, "effect.Am"=NA, "effect.D"=NA)
   } else {
-    qtl.df <- merge(QTLest, CI, by=c("Trait", "linkage.group", "position"), all=TRUE)
+    qtl.df <- merge(QTLest, CI, by=c("Trait", "linkage.group", "position"), all=FALSE)
     if(all(is.numeric(qtl.df[,c("LOD", "perc.var")])))
       qtl.df[,c("LOD", "perc.var")] <- round(qtl.df[,c("LOD", "perc.var")], 2)
     qtl.df <- qtl.df[order(qtl.df$ord),]