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authorzsloan2021-04-27 22:25:44 +0000
committerzsloan2021-04-27 22:25:44 +0000
commit63ca33f75fcb67ba8c3851c60088b62becb5f735 (patch)
treedacdbd0e8c7ed5c4d926365271b78bb5021375f7 /wqflask
parent1845086220e427ed38d1bb2b216dc53de3760d64 (diff)
downloadgenenetwork2-63ca33f75fcb67ba8c3851c60088b62becb5f735.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.py2
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)