diff options
| -rw-r--r-- | scripts/rqtl2_wrapper.R | 55 |
1 files changed, 11 insertions, 44 deletions
diff --git a/scripts/rqtl2_wrapper.R b/scripts/rqtl2_wrapper.R index ccbef84..07b9874 100644 --- a/scripts/rqtl2_wrapper.R +++ b/scripts/rqtl2_wrapper.R @@ -39,7 +39,7 @@ if (is.null(opt$input_file)) { } else { input_file = opt$input_file } -(is.null(opt$output_file)){ +if (is.null(opt$output_file)){ stop("You need to provide an output file to write the ouput data") } @@ -49,6 +49,7 @@ input_file_path = file.path(opt$directory, input_file) if (!(file.exists(input_file_path))) { str_glue("The input file {opt$input_file} path does not exists in the directory {opt$directory}") + stop("The input file does not exists the temp directory") } else { str_glue("The input path for the metadata >>>>>>> {input_file_path}") json_data = fromJSON(file = input_file_path) @@ -223,9 +224,9 @@ print(Xcovar) cat("Computing the kinship") -if (method == "LMM"){ +if (opt$method == "LMM"){ kinship = calc_kinship(genome_prob) -} else if (method == "LOCO"){ +} else if (opt$method == "LOCO"){ kinship = calc_kinship(genome_prob, "loco") }else { kinship = NULL @@ -364,7 +365,7 @@ perform_permutation_test <- function(cross, #' Function to peform permutation tests for single QTL method #' @description The scan1perm() function takes the #' same arguments as scan1(), plus additional a #rguments to control the permutations: - #" @param cross the cross object required to fetch the pheno + #' @param cross the cross object required to fetch the pheno #' @param genome_prob the genomic probability matrix #' @param method to computation method used to perform the genomic scan #' @param intcovar @@ -375,26 +376,8 @@ perform_permutation_test <- function(cross, #' @param n_perm Number of permutation replicates. #' @param chr_lengths engths of the chromosomes; #' @return object of class "scan1perm". - # TODO! add chr_lengths and perm_Xsp - - cat("performing permutation test for the cross object\n") - if (method == "HK") { - perm <- scan1perm( - genome_prob, - cross$pheno, - Xcovar = Xcovar, - intcovar = intcovar, - addcovar = addcovar, - n_perm = n_perm, - model = model, - perm_Xsp = perm_Xsp, - perm_strata = perm_strata, - chr_lengths = chr_lengths, - cores = NO_OF_CORES - ) - } - else if (method == "LMM") { - perm <- scan1perm( + cat("performing permutation test for the cross object\n") + return (scan1perm( genome_prob, cross$pheno, kinship = kinship, @@ -406,27 +389,11 @@ perform_permutation_test <- function(cross, model = model, chr_lengths = chr_lengths, cores = NO_OF_CORES - ) - } - else if (method == "LOCO") { - perm <- scan1perm( - genome_prob, - cross$pheno, - kinship = kinship , - perm_strata = perm_strata, - Xcovar = Xcovar, - intcovar = intcovar, - addcovar = addcovar, - n_perm = n_perm, - perm_Xsp = perm_Xsp, - model = model, - chr_lengths = chr_lengths, - cores = NO_OF_CORES - ) - } - return (perm) + )) } + + # TODO ! get these parameters from argument from the user perm <- perform_permutation_test(dataset, Pr, n_perm = NO_OF_PERMUTATION, method = "LMM") # get the permutation summary with a significance threshold @@ -441,7 +408,7 @@ lod_significance <- get_lod_significance(perm) # get the lod peaks -# fix issue with map +# TODO fix issue when fetching the gmap or allow to use pseudomarkers cat("Fetching the lod peaks\n") lod_peaks = find_peaks( |