diff options
| -rw-r--r-- | scripts/rqtl2_wrapper.R | 7 |
1 files changed, 2 insertions, 5 deletions
diff --git a/scripts/rqtl2_wrapper.R b/scripts/rqtl2_wrapper.R index f514e73..6581ed4 100644 --- a/scripts/rqtl2_wrapper.R +++ b/scripts/rqtl2_wrapper.R @@ -9,7 +9,6 @@ library(stringr) library(optparse) - option_list <- list( make_option(c("-c", "--cores"), type="integer", default=1, help="No of cores to use while making computation"), @@ -306,7 +305,7 @@ perform_genome_scan <- function(cross, cat("Performing scan1 using Haley Knott\n") out <- scan1(genome_prob, cross$pheno, - addcovar = covar, + addcovar = NULL, intcovar = intcovar, model = model, Xcovar = Xcovar, @@ -437,9 +436,7 @@ 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("Fetch the lod with significance thresholds ") - cat(threshold) - cat("\n") + cat("Fetch the lod with significance thresholds ", threshold, "\n") summary(perm, alpha = threshold) } lod_significance <- get_lod_significance(perm) |