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authorzsloan2021-07-22 23:47:58 +0000
committerzsloan2022-03-22 19:03:23 +0000
commite13e10d0f0dc96518e1d5efa9865ac2821b1c3f9 (patch)
treed48fc8971da7738ca7d1edc285eca4e003eeecf7 /scripts/rqtl_wrapper.R
parent7b2901817a1aabd947483f87b5a2a2d33618de7e (diff)
downloadgenenetwork3-e13e10d0f0dc96518e1d5efa9865ac2821b1c3f9.tar.gz
Added option for running pairscan to rqtl_wrapper.R
Diffstat (limited to 'scripts/rqtl_wrapper.R')
-rw-r--r--scripts/rqtl_wrapper.R1
1 files changed, 1 insertions, 0 deletions
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)"),