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| author | zsloan | 2022-05-31 17:55:58 +0000 |
|---|---|---|
| committer | zsloan | 2022-05-31 17:56:56 +0000 |
| commit | 89a7868175c7594be91d638974ac1054fc3c8659 (patch) | |
| tree | 9ef398da62f66621b0a2e4b292b584ab54e8ef90 | |
| parent | b8a51a5d77175f8b88583a06a0ce7e2792bc501f (diff) | |
| download | genenetwork2-89a7868175c7594be91d638974ac1054fc3c8659.tar.gz | |
Reverse polarity for gemma additive effects
This is basically just a quick pseudo-fix to at least get the polarity
right
| -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 623ab87f..ec12f9b7 100644 --- a/wqflask/wqflask/marker_regression/gemma_mapping.py +++ b/wqflask/wqflask/marker_regression/gemma_mapping.py @@ -220,7 +220,7 @@ def parse_loco_output(this_dataset, gwa_output_filename, loco="True"): marker['chr'] = line.split("\t")[0] marker['Mb'] = float(line.split("\t")[2]) / 1000000 marker['p_value'] = float(line.split("\t")[10]) - marker['additive'] = float(line.split("\t")[7]) + marker['additive'] = -(float(line.split("\t")[7])) if math.isnan(marker['p_value']) or (marker['p_value'] <= 0): marker['lod_score'] = 0 else: |