diff options
Diffstat (limited to 'scripts/rqtl2_wrapper.R')
| -rw-r--r-- | scripts/rqtl2_wrapper.R | 16 |
1 files changed, 13 insertions, 3 deletions
diff --git a/scripts/rqtl2_wrapper.R b/scripts/rqtl2_wrapper.R index 07b9874..966d3c6 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 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("-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("-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") ) @@ -394,8 +395,17 @@ perform_permutation_test <- function(cross, -# TODO ! get these parameters from argument from the user -perm <- perform_permutation_test(dataset, Pr, n_perm = NO_OF_PERMUTATION, method = "LMM") + +# check if pstrata + +if (!(is.null(opt$pstrata)) && (!is.null(Xcovar))){ +perm_strata <- mat2strata(Xcovar) +} else { +perm_strata <- NULL +} + +perm <- perform_permutation_test(dataset, Pr, n_perm = NO_OF_PERMUTATION,perm_strata = perm_strata, method = "LMM") + # get the permutation summary with a significance threshold get_lod_significance <- function(perm, threshold = c(0.2, 0.05)){ cat("Fetch the lod with significance thresholds ") |