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| author | Alexander_Kabui | 2025-02-20 13:06:38 +0300 |
|---|---|---|
| committer | Alexander_Kabui | 2025-02-20 13:06:38 +0300 |
| commit | 7bd0fd6d86db897fe91414edb672c7e811a8e1db (patch) | |
| tree | 096256e987d03040de014ec674ffd6afeaf07e58 | |
| parent | 99fd5070a84f37f91993f329f9cc8dd82a4b9339 (diff) | |
| download | genenetwork3-7bd0fd6d86db897fe91414edb672c7e811a8e1db.tar.gz | |
refactor: Use p=0.63 in permutation summary for suggestive threshold.
| -rw-r--r-- | scripts/rqtl2_wrapper.R | 2 |
1 files changed, 1 insertions, 1 deletions
diff --git a/scripts/rqtl2_wrapper.R b/scripts/rqtl2_wrapper.R index 7cad7d5..52a37be 100644 --- a/scripts/rqtl2_wrapper.R +++ b/scripts/rqtl2_wrapper.R @@ -434,7 +434,7 @@ get_lod_significance <- function(perm, threshold = c(0.01, 0.05)){ summary(perm, alpha = threshold) } -lod_significance <- get_lod_significance(perm, threshold =c(0.33, 0.05, 0.01)) +lod_significance <- get_lod_significance(perm, threshold =c(0.63, 0.05, 0.01)) permutation_results_file = file.path(opt$directory, "permutation.csv") significance_results_file = file.path(opt$directory, "significance.csv") write.csv(lod_significance, significance_results_file) |