diff options
| -rw-r--r-- | scripts/rqtl2_wrapper.R | 28 |
1 files changed, 28 insertions, 0 deletions
diff --git a/scripts/rqtl2_wrapper.R b/scripts/rqtl2_wrapper.R index 9d288af..92cfd52 100644 --- a/scripts/rqtl2_wrapper.R +++ b/scripts/rqtl2_wrapper.R @@ -160,6 +160,7 @@ perform_genetic_pr <- function(cross, cores = NO_OF_CORES, step = 1, map = NULL, # Insert pseudomarkers to the genetic map cat("Inserting pseudomarkers to the genetic map with step 1 and stepwidth fixed.\n") + MAP <- insert_pseudomarkers(cross$gmap, step = 1, stepwidth = "fixed", cores = NO_OF_CORES) # Calculate genetic probabilities @@ -307,12 +308,39 @@ get_qtl_effect <- function(chromosome, geno_prob, pheno, covar = NULL, LOCO = NU gmap_file <- file.path(opt$directory, json_data$geno_map_file) pmap_file <- file.path(opt$directory, json_data$physical_map_file) + + + + +# Construct the Map object from cross with columns (Marker, chr, cM, Mb) +gmap <- cross$gmap # Genetic map in cM +pmap <- cross$pmap # Physical map in Mb +# Convert lists to data frames +gmap_df <- data.frame( + marker = unlist(lapply(gmap, names)), + chr = rep(names(gmap), sapply(gmap, length)), # Add chromosome info + CM = unlist(gmap), + stringsAsFactors = FALSE +) + +pmap_df <- data.frame( + marker = unlist(lapply(pmap, names)), + chr = rep(names(pmap), sapply(pmap, length)), # Add chromosome info + MB = unlist(pmap), + stringsAsFactors = FALSE +) +# Merge using full outer join (by marker and chromosome) +merged_map <- merge(gmap_df, pmap_df, by = c("marker", "chr"), all = TRUE) +map_file <- file.path(opt$directory, "map.csv") +write.csv(merged_map, map_file, row.names = FALSE) + output <- list( permutation_file = permutation_results_file, significance_file = significance_results_file, scan_file = scan_file, gmap_file = gmap_file, pmap_file = pmap_file, + map_file = map_file, permutations = NO_OF_PERMUTATION, scan_method = SCAN_METHOD ) |