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| author | zsloan | 2021-04-27 22:25:44 +0000 |
|---|---|---|
| committer | zsloan | 2021-04-27 22:25:44 +0000 |
| commit | 63ca33f75fcb67ba8c3851c60088b62becb5f735 (patch) | |
| tree | dacdbd0e8c7ed5c4d926365271b78bb5021375f7 /wqflask | |
| parent | 1845086220e427ed38d1bb2b216dc53de3760d64 (diff) | |
| download | genenetwork2-63ca33f75fcb67ba8c3851c60088b62becb5f735.tar.gz | |
Convert to array and transpose R/qtl scanone results when not using cofactors. For some reason the rows/columns are inverted when converted to a python object when doing scanone with cofactors vs without cofactors
Diffstat (limited to 'wqflask')
| -rw-r--r-- | wqflask/wqflask/marker_regression/rqtl_mapping.py | 2 |
1 files changed, 1 insertions, 1 deletions
diff --git a/wqflask/wqflask/marker_regression/rqtl_mapping.py b/wqflask/wqflask/marker_regression/rqtl_mapping.py index c70fbbec..cd43577e 100644 --- a/wqflask/wqflask/marker_regression/rqtl_mapping.py +++ b/wqflask/wqflask/marker_regression/rqtl_mapping.py @@ -116,7 +116,7 @@ def run_rqtl_geno(vals, samples, dataset, mapping_scale, method, model, permChec result_data_frame = ro.r("qtl_results") else: ro.r(f"qtl_results = scanone(the_cross, pheno='the_pheno', model='{model}', method='{method}')") - result_data_frame = ro.r("qtl_results") + result_data_frame = np.asarray(ro.r("qtl_results")).T marker_names = np.asarray(ro.r("row.names(qtl_results)")) if num_perm > 0 and permCheck == "ON": # Do permutation (if requested by user) |