From 2653d69da1e87ba97a4295b55c0f05a5b7261837 Mon Sep 17 00:00:00 2001 From: Olga Botvinnik Date: Mon, 2 Feb 2015 16:21:42 -0800 Subject: [PATCH] initial commit for adding combat functionality --- flotilla/data_model/study.py | 3 +++ 1 file changed, 3 insertions(+) diff --git a/flotilla/data_model/study.py b/flotilla/data_model/study.py index 40ca054f..c5079acd 100644 --- a/flotilla/data_model/study.py +++ b/flotilla/data_model/study.py @@ -80,6 +80,7 @@ def __init__(self, sample_metadata, version='0.1.0', expression_data=None, expression_log_base=None, expression_thresh=-np.inf, expression_plus_one=False, + expression_correct_batch_effects=False, splicing_data=None, splicing_feature_data=None, splicing_feature_rename_col=None, @@ -100,6 +101,8 @@ def __init__(self, sample_metadata, version='0.1.0', expression_data=None, metadata_phenotype_to_color=None, metadata_phenotype_to_marker=None, metadata_outlier_col=OUTLIER_COL, + metadata_batch_col='batch', + metadata_batch_min_samples=3, license=None, title=None, sources=None, default_sample_subset="all_samples", default_feature_subset="variant",