diff options
| -rw-r--r-- | scripts/rqtl2_wrapper.R | 21 |
1 files changed, 19 insertions, 2 deletions
diff --git a/scripts/rqtl2_wrapper.R b/scripts/rqtl2_wrapper.R index d8cf755..4c1e3dc 100644 --- a/scripts/rqtl2_wrapper.R +++ b/scripts/rqtl2_wrapper.R @@ -307,8 +307,8 @@ generate_lod_plot <- function(cross, scan_result, method, base_dir = ".") { } -lod_file_path <- generate_lod_plot(dataset, scan_results, "HK") -lod_file_path +lod_plot_path <- generate_lod_plot(dataset, scan_results, "HK") +lod_plot_path # perform permutation tests for single-QTL method @@ -421,3 +421,20 @@ lod_peaks = find_peaks( ) lod_peaks +cat("Generating the ouput data as vector\n") +output = list(lod_peaks = lod_peaks, + scan_results =scan_results, + lod_significance = lod_significance, + permutation_results = perm, + lod_peaks = lod_peaks, + lod_plot_path =lod_plot_path, + scan_method = SCAN_METHOD + ) + +output_json_data <-toJSON(output) +file_name = genRandomFileName(prefix = "RQTL_output_", file_ext = ".json") +output_file_path = file.path("." , file_name) +str_glue("The output file path is {output_file_path}") +cat("Writing to the output file\n") +write(output_json_data, file=output_file_path) + |