bug fix write_rqtl

.Rproj.user/shared/notebooks/paths

@@ -16,3 +16,4 @@
 /home/marie/Documents/stuart_package/stuart/README.md="8BBA9900"
 /home/marie/Documents/stuart_package/stuart/man/genos.Rd="383A8DC0"
 /home/marie/Documents/stuart_package/stuart/vignettes/stuaRt.Rmd="007031F6"
+/mnt/gaia/gaia_mouselab/Marie/Package_stuaRt/Article/Figures/Maestro/map_before_neogen/map_before_neogen.R="36D40A63"

R/write_rqtl.R

@@ -60,7 +60,7 @@ write_rqtl <- function(geno,pheno,tab,ref,par1,par2,par_N=TRUE,prefix,pos,path=N
   geno <- left_join(geno,ref,by=c("marker"="marker"))
 
   #remove snps with no position
-  geno <- geno %>% filter(is.na(chr)==FALSE)
+  geno <- geno %>% filter(is.na(chr)==FALSE) %>% filter(is.na(!!sym(pos))==FALSE)
 
   #recode "-" in "N" in geno file
   geno <- geno %>% mutate(allele_1 = recode(allele_1,