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authorzsloan2021-07-22 23:47:58 +0000
committerzsloan2021-09-23 19:28:12 +0000
commite9110f840c8817092d0264990a4c7f6d16e966ba (patch)
tree1d790a92e76dfd7976c269eb433256bb033dfb00 /scripts/rqtl_wrapper.R
parent2cf220a11936125f059dc9b6a494d0f70eac068d (diff)
downloadgenenetwork3-e9110f840c8817092d0264990a4c7f6d16e966ba.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 7518175..db0b83c 100644
--- a/scripts/rqtl_wrapper.R
+++ b/scripts/rqtl_wrapper.R
@@ -11,6 +11,7 @@ option_list = list(
make_option(c("-c", "--addcovar"), action="store_true", default=NULL, help="Use covariates (included as extra columns in the phenotype input file)"),
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)"),