diff options
Diffstat (limited to 'scripts/rqtl2_wrapper.R')
| -rw-r--r-- | scripts/rqtl2_wrapper.R | 27 |
1 files changed, 12 insertions, 15 deletions
diff --git a/scripts/rqtl2_wrapper.R b/scripts/rqtl2_wrapper.R index 31bd2b4..7b83284 100644 --- a/scripts/rqtl2_wrapper.R +++ b/scripts/rqtl2_wrapper.R @@ -10,24 +10,23 @@ library(optparse) option_list <- list( - make_option(c("-c", "--cores"), type="integer", default=1, help="No of cores to use while making - computation"), + make_option(c("-d", "--directory"), action = "store", default = NULL, type = "character", help="Temporary working directory: should also host the input file ."), make_option(c("-i", "--input_file"), action="store", default=NULL, type='character', help="a yaml or json file with required data to create the cross file"), -make_option(c("-p", "--nperm"), type="integer", default= 1, action="store_true", help="No of permutations "), - make_option(c("-d", "--directory"), action = "store", default = NULL, type = "character", help="Temporary working directory: should also host the input file ."), + make_option(c("-o", "--output_file"), action="store", default=NULL, type='character', help="a file path of where to write the output json results"), + make_option(c("-c", "--cores"), type="integer", default=1, help="No of cores to use while making + 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("-o", "--output_file"), action="store", default=NULL, type='character', help="a file name of where to write the output json results"), make_option(c("--pstrata"), action="store_true", default=NULL, help="Use permutation strata") ) - opt <- parse_args(OptionParser(option_list=option_list)) NO_OF_CORES = opt$cores SCAN_METHOD = opt$method NO_OF_PERMUTATION = opt$nperm # Step: check for mandatory file paths -# NOTE this is the working dir should be the path for both INPUT and OUTPUT_FILE +# NOTE this is the working dir where the cross file will be generated # NOTE this is where the cross file is generated if(is.null(opt$directory) || !(dir.exists(opt$directory))){ @@ -35,17 +34,17 @@ if(is.null(opt$directory) || !(dir.exists(opt$directory))){ stop("The working directory does not exists or is NULL\n") } -INPUT_FILE_PATH = file.path(opt$directory, opt$input_file) -OUTPUT_FILE_PATH = file.path(opt$directory , opt$output_file) +INPUT_FILE_PATH = opt$input_file +OUTPUT_FILE_PATH = opt$output_file if (!(file.exists(INPUT_FILE_PATH))) { - stop("The input file", INPUT_FILE_PATH, " you provided does not exists the directory", opt$directory, "\n") + 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))) { - stop("The output file ",OUTPUT_FILE_PATH, " you provided does not exists in the directory", opt$directory, "\n") + stop("The output file ",OUTPUT_FILE_PATH, " you provided does not exists\n") } else { cat("Output file exists ...", OUTPUT_FILE_PATH, "\n") } @@ -92,7 +91,7 @@ if (!(item %in% names(json_data))){ - +# Note the files below should be in the same directory as the location for the crosss file generate_cross_object <- function(control_file_path, json_data) { # function to write the cross object from a json data object return ( @@ -308,13 +307,11 @@ perform_genome_scan <- function(cross, } # Perform the genome scan for the cross object - - if (dataset$crosstype == "4way"){ sex <- (DOex$covar$Sex == "male")*1 names(sex) <- rownames(dataset$covar) sex <- setNames( (dataset$covar$Sex == "male")*1, rownames(DOex$covar)) - scan_results <- perform_genoeme_scan(aPr, dataset, kinship=kinship, method = "LOCO", addcovar = sex) + scan_results <- perform_genome_scan(aPr, dataset, kinship=kinship, method = "LOCO", addcovar = sex) } else { scan_results <- perform_genome_scan(cross = dataset, genome_prob = Pr, |