From 516d90d52fbca624dcc4eb15bf8fee9968620845 Mon Sep 17 00:00:00 2001 From: adamgayoso Date: Mon, 21 Dec 2020 08:35:49 -0800 Subject: [PATCH] remove all p values --- doubletdetection/doubletdetection.py | 10 +++------- 1 file changed, 3 insertions(+), 7 deletions(-) diff --git a/doubletdetection/doubletdetection.py b/doubletdetection/doubletdetection.py index fb8f4fb..94e05c9 100644 --- a/doubletdetection/doubletdetection.py +++ b/doubletdetection/doubletdetection.py @@ -58,11 +58,8 @@ class BoostClassifier: Attributes: all_log_p_values_ (ndarray): Hypergeometric test natural log p-value per - cell for cluster enrichment of synthetic doublets. Shape (n_iters, - num_cells). - all_p_values_ (ndarray): DEPRECATED. Exponentiated all_log_p_values. - Due to rounding point errors, use of all_log_p_values recommended. - Will be removed in v3.0. + cell for cluster enrichment of synthetic doublets. Use for tresholding. + Shape (n_iters, num_cells). all_scores_ (ndarray): The fraction of a cell's cluster that is synthetic doublets. Shape (n_iters, num_cells). communities_ (ndarray): Cluster ID for corresponding cell. Shape @@ -149,7 +146,7 @@ def fit(self, raw_counts): raw_counts (array-like): Count matrix, oriented cells by genes. Sets: - all_scores_, all_p_values_, all_log_p_values_, communities_, + all_scores_, all_log_p_values_, communities_, top_var_genes, parents, synth_communities Returns: @@ -220,7 +217,6 @@ def fit(self, raw_counts): self.communities_ = all_communities self.parents_ = all_parents self.synth_communities_ = all_synth_communities - self.all_p_values_ = np.exp(self.all_log_p_values_) return self