Revised the format of the output of scan1 to no longer include the map of marker/pseudomarker positions. You now need to provide both the scan1 output and the genetic map when doing plots or getting summaries.
Also, in SNP association analyses, there's an extra step with index_snps() to identify the subset of non-equivalent SNPs.
Revised the format of the output of
scan1to no longer include the map of marker/pseudomarker positions. You now need to provide both thescan1output and the genetic map when doing plots or getting summaries.Also, in SNP association analyses, there's an extra step with
index_snps()to identify the subset of non-equivalent SNPs.See http://kbroman.org/qtl2/assets/vignettes/version05_new.html.