diff options
| -rw-r--r-- | scripts/rqtl2_wrapper.R | 15 |
1 files changed, 12 insertions, 3 deletions
diff --git a/scripts/rqtl2_wrapper.R b/scripts/rqtl2_wrapper.R index 6477f94..accf3fa 100644 --- a/scripts/rqtl2_wrapper.R +++ b/scripts/rqtl2_wrapper.R @@ -6,7 +6,6 @@ library(rjson) library(stringi) library(optparse) -# TODO add mapping function as a parameter: option_list <- list( make_option(c("-d", "--directory"), action = "store", default = NULL, type = "character", help="Temporary working directory: should also host the input file ."), @@ -186,7 +185,7 @@ MAP <- insert_pseudomarkers(cross$gmap, step= 1, stepwidth = "fixed", cores = NO # Step: calculate the genetic probabilities cat("Calculating the genetic probabilities\n") -Pr = perform_genetic_pr(cross, map = MAP) +Pr = perform_genetic_pr(cross) @@ -321,6 +320,12 @@ if (cross$crosstype == "4way"){ kinship = kinship, method = SCAN_METHOD) } + + + +scan_file <- file.path(opt$directory, "scan_results.csv") +write.csv(scan_results, scan_file) + # function plot for the LOD scores from performing the genome scan generate_lod_plot <- function(cross, scan_result, method, base_dir = ".") { #' @description Plot LOD curves for a genome scan @@ -469,6 +474,7 @@ get_qtl_effect <- function(chromosome,geno_prob,pheno,covar=NULL,LOCO= NULL){ # take the first phenotype in the cross # grab phenotypes and covariates; ensure that covariates have names attribute + pheno <- cross$pheno[,1] if (!is.null(cross$covar) && !is.null(cross$covar$sex)){ covar <- match(cross$covar$sex, c("f", "m")) # make numeric @@ -506,6 +512,8 @@ for (chr in chr_names(cross)){ } + +gmap_file <- file.path(opt$directory, json_data$geno_map_file) output = list(lod_peaks = lod_peaks, scan_results =scan_results, genetic_probabilities = Pr, @@ -514,9 +522,10 @@ output = list(lod_peaks = lod_peaks, lod_peaks = lod_peaks, permutation_file = permutation_results_file, significance_file = significance_results_file, + scan_file = scan_file, chromosomes = chr_names(cross), - meffects = meffects, error_lod = error_lod, + gmap_file = gmap_file, meffects_plots = meffects_plots, lod_plot_path =lod_plot_path, scan_method = SCAN_METHOD |