diff options
| author | Frederick Muriuki Muriithi | 2021-12-14 04:37:15 +0300 |
|---|---|---|
| committer | Frederick Muriuki Muriithi | 2021-12-14 04:37:15 +0300 |
| commit | 1a46021a37ca23fe9893fd4ac9ac9c1d4066884b (patch) | |
| tree | 3162218579654d749bdb3a8ace12122d0996eaa5 /gn3/computations | |
| parent | f81950baa398212861200dbc088b80dbdcc4fead (diff) | |
| download | genenetwork3-1a46021a37ca23fe9893fd4ac9ac9c1d4066884b.tar.gz | |
Remove any items with less than 3 samples
Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* pingouin raises an exception whenever one attempts to use it to compute the
partial correlation with data that has less than 3 samples.
Diffstat (limited to 'gn3/computations')
| -rw-r--r-- | gn3/computations/partial_correlations.py | 7 |
1 files changed, 6 insertions, 1 deletions
diff --git a/gn3/computations/partial_correlations.py b/gn3/computations/partial_correlations.py index 87d0201..fbff4df 100644 --- a/gn3/computations/partial_correlations.py +++ b/gn3/computations/partial_correlations.py @@ -306,6 +306,9 @@ def compute_partial( prim for targ, prim in zip(targ_vals, primary_vals) if targ is not None] + if len(primary) < 3: + return None + def __remove_controls_for_target_nones(cont_targ): return tuple(cont for cont,targ in cont_targ if targ is not None) @@ -338,8 +341,10 @@ def compute_partial( zero_order_corr["r"][0], zero_order_corr["p-val"][0]) return tuple( - __compute_trait_info__(target) + result for result in ( + __compute_trait_info__(target) for target in zip(target_vals, target_names)) + if result is not None) def partial_correlations_normal(# pylint: disable=R0913 primary_vals, control_vals, input_trait_gene_id, trait_database, |