Update write_rqtl.R

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"))