diff options
Diffstat (limited to 'scripts/rqtl2_wrapper.R')
| -rw-r--r-- | scripts/rqtl2_wrapper.R | 22 |
1 files changed, 9 insertions, 13 deletions
diff --git a/scripts/rqtl2_wrapper.R b/scripts/rqtl2_wrapper.R index 7b83284..ee56d90 100644 --- a/scripts/rqtl2_wrapper.R +++ b/scripts/rqtl2_wrapper.R @@ -20,7 +20,8 @@ make_option(c("-i", "--input_file"), action="store", default=NULL, type='charact make_option(c("--pstrata"), action="store_true", default=NULL, help="Use permutation strata") ) -opt <- parse_args(OptionParser(option_list=option_list)) +opt_parser = OptionParser(option_list=option_list); +opt <- parse_args(opt_parser) NO_OF_CORES = opt$cores SCAN_METHOD = opt$method NO_OF_PERMUTATION = opt$nperm @@ -36,14 +37,14 @@ stop("The working directory does not exists or is NULL\n") INPUT_FILE_PATH = opt$input_file OUTPUT_FILE_PATH = opt$output_file - if (!(file.exists(INPUT_FILE_PATH))) { + print_help(opt_parser) stop("The input file", INPUT_FILE_PATH, " you provided does not exists\n") } else { cat("Input file exists Reading the input file .... \n") - } if (!(file.exists(OUTPUT_FILE_PATH))) { + print_help(opt_parser) stop("The output file ",OUTPUT_FILE_PATH, " you provided does not exists\n") } else { cat("Output file exists ...", OUTPUT_FILE_PATH, "\n") @@ -57,9 +58,6 @@ genRandomFileName <- function(prefix, string_size = 9 , file_ext = ".txt") { } - - - # Step: Generate the control file name control_file_path <- file.path(opt$directory, genRandomFileName(prefix = "control", file_ext = ".json")) @@ -422,12 +420,11 @@ perm <- perform_permutation_test(dataset, Pr, n_perm = NO_OF_PERMUTATION,perm_st # get the permutation summary with a significance threshold get_lod_significance <- function(perm, threshold = c(0.2, 0.05)){ - cat("Fetching the lod with significance thresholds as ", threshold, "\n") - summary(perm, alpha = threshold) + cat("Getting the permutation summary with significance thresholds as ", threshold, "\n") + summary(perm, alpha = threshold) } -lod_significance <- get_lod_significance(perm) - +lod_significance <- get_lod_significance(perm) # step: get the lod peaks # TODO fix the threshold here @@ -472,7 +469,7 @@ if (!is.null(dataset$covar) && !is.null(dataset$covar$sex)){ } else { covar <- NULL } -covar + meffects <- c() @@ -499,8 +496,7 @@ for (chr in chr_names(dataset)){ meffects <- append(meffects_plots, image_loc) } else { coeff_results <- get_qtl_effect(chr, Pr, pheno) - } - + } meffects <- append(meffects, coeff_results) } output = list(lod_peaks = lod_peaks, |