From 77caa6a460d9ac6d104d9c85c973bae74064e812 Mon Sep 17 00:00:00 2001
From: hanna julienne <hanna.julienne@pasteur.fr>
Date: Tue, 29 Oct 2019 14:46:28 +0100
Subject: [PATCH] corrected sumZ and added pleiotropy index
---
jass/models/stats.py | 1 -
jass/models/worktable.py | 14 +++++++++++++-
2 files changed, 13 insertions(+), 2 deletions(-)
diff --git a/jass/models/stats.py b/jass/models/stats.py
index d64a581c..c25bb57c 100755
--- a/jass/models/stats.py
+++ b/jass/models/stats.py
@@ -108,7 +108,6 @@ def omnibus_stat(z, cov, invcov):
omnibus_stat.can_use_pattern = True
-
def fisher_test(z, cov, invcov):
"""
fisher combination of univariate p-values corrected with bonferoni
diff --git a/jass/models/worktable.py b/jass/models/worktable.py
index e1b5fb78..3f1feac6 100755
--- a/jass/models/worktable.py
+++ b/jass/models/worktable.py
@@ -122,6 +122,15 @@ def post_computation_filtering(worktable_chunk, significant_treshold = 5*10**-8)
return worktable_chunk
+def compute_pleiotropy_index(W,significance_treshold):
+
+ N_significatif = (2.0 * spst.norm.sf(W.fillna(0, inplace=False).abs())<significance_treshold).sum(1)
+ N_pheno = (~W.isnull()).sum(1)
+ #pleiotropy index is not meaningful for too few phenotype
+ S = N_significatif/N_pheno
+ S.loc[N_pheno < 4] = np.nan
+ return S
+
def create_worktable_file(
phenotype_ids: List[str],
init_file_path: str,
@@ -255,8 +264,11 @@ def create_worktable_file(
sum_stat_tab["UNIVARIATE_MIN_QVAL"] = sum_stat_tab["UNIVARIATE_MIN_PVAL"]*(1-np.isnan(sum_stat_tab[phenotype_ids]).astype(int)).sum(1)
sum_stat_tab.loc[sum_stat_tab.UNIVARIATE_MIN_QVAL>1 , "UNIVARIATE_MIN_QVAL"] = 1
+ #Computing pleiotropy
+ sum_stat_tab["PLEIOTROPY_INDEX"] = compute_pleiotropy_index(sum_stat_tab[phenotype_ids], significance_treshold)
+
sum_stat_tab = sum_stat_tab[
- ["Region", "CHR", "snp_ids", "position", 'Ref_allele', 'Alt_allele', "MiddlePosition", "JASS_PVAL", "UNIVARIATE_MIN_PVAL", "UNIVARIATE_MIN_QVAL"]
+ ["Region", "CHR", "snp_ids", "position", 'Ref_allele', 'Alt_allele', "MiddlePosition", "JASS_PVAL", "UNIVARIATE_MIN_PVAL", "UNIVARIATE_MIN_QVAL","PLEIOTROPY_INDEX" ]
+ phenotype_ids]
if post_filtering:
--
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