diff options
| author | Alexander_Kabui | 2024-11-11 12:04:42 +0300 |
|---|---|---|
| committer | Alexander_Kabui | 2024-11-11 12:04:42 +0300 |
| commit | 0a5c1f7d4ccc88d3555e44b50beec8ee91bc43fc (patch) | |
| tree | 23031c0c14e851e41dc345ceeb5b5da49e5e8f2f /scripts/rqtl2_wrapper.R | |
| parent | 5494e2ba34bafb7820cf1d578d34302a39eb9811 (diff) | |
| download | genenetwork3-0a5c1f7d4ccc88d3555e44b50beec8ee91bc43fc.tar.gz | |
refactor: refactor printing out lod thresholds.
Diffstat (limited to 'scripts/rqtl2_wrapper.R')
| -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) |