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| author | zsloan | 2021-07-22 23:47:58 +0000 |
|---|---|---|
| committer | zsloan | 2021-07-22 23:47:58 +0000 |
| commit | 238e3a1cfd4bc8677a530410af2767d28e93af62 (patch) | |
| tree | d0ade5b969cba349aabde6b0b205cc9de58a8990 /scripts | |
| parent | 7d22039c2ae0aef6abc575008f11b95e555e3e9a (diff) | |
| download | genenetwork3-238e3a1cfd4bc8677a530410af2767d28e93af62.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 f7e0406..98b1231 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)"), |