diff options
| -rw-r--r-- | scripts/rqtl2_wrapper.R | 2 |
1 files changed, 2 insertions, 0 deletions
diff --git a/scripts/rqtl2_wrapper.R b/scripts/rqtl2_wrapper.R index 69606b2..5ad812e 100644 --- a/scripts/rqtl2_wrapper.R +++ b/scripts/rqtl2_wrapper.R @@ -514,6 +514,7 @@ for (chr in chr_names(cross)){ gmap_file <- file.path(opt$directory, json_data$geno_map_file) +pmap_file <- file.path(opt$directory, json_data$physical_map_file) output = list(lod_peaks = lod_peaks, scan_results =scan_results, genetic_probabilities = Pr, @@ -526,6 +527,7 @@ output = list(lod_peaks = lod_peaks, chromosomes = chr_names(cross), error_lod = error_lod, gmap_file = gmap_file, + pmap_file = pmap_file, meffects_plots = meffects_plots, lod_plot_path =lod_plot_path, scan_method = SCAN_METHOD |