From e13e10d0f0dc96518e1d5efa9865ac2821b1c3f9 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Thu, 22 Jul 2021 23:47:58 +0000
Subject: Added option for running pairscan to rqtl_wrapper.R

---
 scripts/rqtl_wrapper.R | 1 +
 1 file changed, 1 insertion(+)

(limited to 'scripts')

diff --git a/scripts/rqtl_wrapper.R b/scripts/rqtl_wrapper.R
index 13c2684..4c96ff2 100644
--- a/scripts/rqtl_wrapper.R
+++ b/scripts/rqtl_wrapper.R
@@ -12,6 +12,7 @@ option_list = list(
   make_option(c("--covarstruct"), type="character", help="File detailing which covariates are categorical or numerical"),
   make_option(c("--model"), type="character", default="normal", help="Mapping Model - Normal or Non-Parametric"),
   make_option(c("--method"), type="character", default="hk", help="Mapping Method - hk (Haley Knott), ehk (Extended Haley Knott), mr (Marker Regression), em (Expectation-Maximization), imp (Imputation)"),
+  make_option(c("--pairscan"), action="store_true", default=NULL, help="Run Pair Scan - the R/qtl function scantwo"),
   make_option(c("-i", "--interval"), action="store_true", default=NULL, help="Use interval mapping"),
   make_option(c("--nperm"), type="integer", default=0, help="Number of permutations"),
   make_option(c("--pstrata"), action="store_true", default=NULL, help="Use permutation strata (stored as final column/vector in phenotype input file)"),
-- 
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