diff options
| -rw-r--r-- | scripts/rqtl2_wrapper.R | 13 |
1 files changed, 6 insertions, 7 deletions
diff --git a/scripts/rqtl2_wrapper.R b/scripts/rqtl2_wrapper.R index ee56d90..753a88d 100644 --- a/scripts/rqtl2_wrapper.R +++ b/scripts/rqtl2_wrapper.R @@ -17,7 +17,8 @@ make_option(c("-i", "--input_file"), action="store", default=NULL, type='charact computation"), make_option(c("-p", "--nperm"), type="integer", default= 1, action="store_true", help="No of permutations "), make_option(c("-m", "--method"), action = "store", default = "HK", type = "character", help="Scan Mapping Method - HK (Haley Knott), LMM( Linear Mixed Model ), LOCO (Leave one Chromosome Out)"), - make_option(c("--pstrata"), action="store_true", default=NULL, help="Use permutation strata") + make_option(c("--pstrata"), action="store_true", default=NULL, help="Use permutation strata"), + make_option(c("-t", "--threshold"), type="integer", default= 1, action="store_true", help="Minimum LOD score for a Peak") ) opt_parser = OptionParser(option_list=option_list); @@ -32,7 +33,8 @@ NO_OF_PERMUTATION = opt$nperm if(is.null(opt$directory) || !(dir.exists(opt$directory))){ # check if directory exists -stop("The working directory does not exists or is NULL\n") + print_help(opt_parser) + stop("The working directory does not exists or is NULL\n") } INPUT_FILE_PATH = opt$input_file @@ -430,10 +432,10 @@ lod_significance <- get_lod_significance(perm) # TODO fix the threshold here -cat("Fetching the lod peaks\n") +cat("Fetching the lod peaks with threshold", opt$threshold, "\n") lod_peaks = find_peaks( scan_results, - threshold =0, + threshold =opt$threshold, map = dataset$gmap, cores = NO_OF_CORES ) @@ -461,7 +463,6 @@ get_qtl_effect <- function(chromosome,geno_prob,pheno,covar=NULL,LOCO= NULL){ # take the first phenotype in the dataset # grab phenotypes and covariates; ensure that covariates have names attribute - pheno <- dataset$pheno[,1] if (!is.null(dataset$covar) && !is.null(dataset$covar$sex)){ covar <- match(dataset$covar$sex, c("f", "m")) # make numeric @@ -470,8 +471,6 @@ if (!is.null(dataset$covar) && !is.null(dataset$covar$sex)){ covar <- NULL } - - meffects <- c() meffects_plots <- c() # TODO add plots for meffects |