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| author | zsloan | 2021-07-22 23:47:58 +0000 |
|---|---|---|
| committer | zsloan | 2022-03-22 19:03:23 +0000 |
| commit | e13e10d0f0dc96518e1d5efa9865ac2821b1c3f9 (patch) | |
| tree | d48fc8971da7738ca7d1edc285eca4e003eeecf7 /scripts | |
| parent | 7b2901817a1aabd947483f87b5a2a2d33618de7e (diff) | |
| download | genenetwork3-e13e10d0f0dc96518e1d5efa9865ac2821b1c3f9.tar.gz | |
Added option for running pairscan to rqtl_wrapper.R
Diffstat (limited to 'scripts')
| -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)"), |