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| author | zsloan | 2023-11-25 20:19:25 +0000 |
|---|---|---|
| committer | zsloan | 2023-11-25 20:19:42 +0000 |
| commit | 8f303cfc8a7bfc3c2520f1706c249485c848ce98 (patch) | |
| tree | 0685c0540150d8b9d199b8aa8ff42b57304b6331 | |
| parent | c69294efd979bc117218f247b0ce058893603018 (diff) | |
| download | genenetwork2-8f303cfc8a7bfc3c2520f1706c249485c848ce98.tar.gz | |
Fix bug caused by NaN p-values in GEMMA mapping
| -rw-r--r-- | wqflask/wqflask/marker_regression/gemma_mapping.py | 2 |
1 files changed, 1 insertions, 1 deletions
diff --git a/wqflask/wqflask/marker_regression/gemma_mapping.py b/wqflask/wqflask/marker_regression/gemma_mapping.py index 5d424c97..47ad5638 100644 --- a/wqflask/wqflask/marker_regression/gemma_mapping.py +++ b/wqflask/wqflask/marker_regression/gemma_mapping.py @@ -234,7 +234,7 @@ def parse_loco_output(this_dataset, gwa_output_filename, loco="True"): marker['p_value'] = float(line.split("\t")[10]) marker['additive'] = -(float(line.split("\t")[7])/2) if math.isnan(marker['p_value']) or (marker['p_value'] <= 0): - marker['lod_score'] = 0 + marker['lod_score'] = marker['p_value'] = 0 else: marker['lod_score'] = -math.log10(marker['p_value']) marker_obs.append(marker) |