From 3afae76c7911aa884b7df8fa575f8dc69191911f Mon Sep 17 00:00:00 2001
From: Marie BOURDON <marie.bourdon@pasteur.fr>
Date: Thu, 17 Jun 2021 11:34:32 +0000
Subject: [PATCH] Update write_rqtl.R
---
R/write_rqtl.R | 3 +++
1 file changed, 3 insertions(+)
diff --git a/R/write_rqtl.R b/R/write_rqtl.R
index 0926c5c..ff77d82 100755
--- a/R/write_rqtl.R
+++ b/R/write_rqtl.R
@@ -59,6 +59,9 @@ write_rqtl <- function(geno,pheno,tab,ref,par1,par2,prefix,pos,path=NA){
#merge genotypes with parents
geno <- left_join(geno,ref,by=c("marker"="marker"))
+ #remove snps with no position
+ geno <- geno %>% filter(is.na(chr)==FALSE)
+
#recode "-" in "N" in geno file
geno <- geno %>% mutate(allele_1 = recode(allele_1,
"-" = "N"))
--
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