From b023a80e0223741cabc7b805f2f8328049246241 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?G=C3=B6k=C3=A7en=20Eraslan?= Date: Mon, 7 Oct 2019 14:31:34 -0400 Subject: [PATCH 1/3] Fix versus_rest link --- docs/tutorials.rst | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/docs/tutorials.rst b/docs/tutorials.rst index 95ee021..25c5ee9 100644 --- a/docs/tutorials.rst +++ b/docs/tutorials.rst @@ -32,7 +32,8 @@ Multiple tests per gene How to perform pairwise tests `pairwise `__. -How to perform group versus rest tests `versus_rest `__. +How to perform group versus rest tests `versus_rest +`__. Gene set enrichment: enrich From c27eead881f9857fafe3da82e8bbc8d76d618999 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?G=C3=B6k=C3=A7en=20Eraslan?= Date: Mon, 7 Oct 2019 14:33:44 -0400 Subject: [PATCH 2/3] Remove whitespace --- docs/tutorials.rst | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/docs/tutorials.rst b/docs/tutorials.rst index 25c5ee9..e7b79e0 100644 --- a/docs/tutorials.rst +++ b/docs/tutorials.rst @@ -32,8 +32,7 @@ Multiple tests per gene How to perform pairwise tests `pairwise `__. -How to perform group versus rest tests `versus_rest -`__. +How to perform group versus rest tests `versus_rest `__. Gene set enrichment: enrich From 838ceb1229ee188ffe569f6194ae16035b713299 Mon Sep 17 00:00:00 2001 From: le-ander <20015434+le-ander@users.noreply.github.com> Date: Thu, 30 Jul 2020 12:52:34 +0200 Subject: [PATCH 3/3] fix extraction of corf_loc_names when dmat is provided directly --- diffxpy/testing/tests.py | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/diffxpy/testing/tests.py b/diffxpy/testing/tests.py index c378494..6c208ce 100644 --- a/diffxpy/testing/tests.py +++ b/diffxpy/testing/tests.py @@ -694,7 +694,10 @@ def wald( as_numeric=as_numeric ) else: - coef_loc_names = dmat_loc.columns.tolist() + if isinstance(dmat_loc, patsy.design_info.DesignMatrix): + coef_loc_names = dmat_loc.design_info.column_names + else: + coef_loc_names = dmat_loc.columns.tolist() if not np.all([x in coef_loc_names for x in coef_to_test]): raise ValueError( "the requested test coefficients %s were found in model coefficients %s" %