diff options
| -rw-r--r-- | scripts/rqtl_wrapper.R | 1 |
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)"), |