Merge pull request #178 from monarch-initiative/more_mtc_heuristic

More mtc heuristic
monarch-initiative · Jul 3, 2024 · 5542961 · 5542961
2 parents f3d02c1 + 567abab
commit 5542961
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Showing 10 changed files with 305 additions and 257 deletions.
diff --git a/notebooks/MAPK8IP3/MAPK8IP3.ipynb b/notebooks/MAPK8IP3/MAPK8IP3.ipynb
@@ -418,8 +418,7 @@
     "analysis_config = CohortAnalysisConfiguration()\n",
     "analysis_config.missing_implies_excluded = True\n",
     "analysis_config.pval_correction = 'fdr_bh'\n",
-    "analysis_config.min_perc_patients_w_hpo = 0.1\n",
-    "analysis_config.heuristic_strategy()\n",
+    "analysis_config.heuristic_strategy(threshold_HPO_observed_frequency=0.25)\n",
     "analysis = configure_cohort_analysis(cohort, hpo, config=analysis_config)"
    ]
   },

diff --git a/notebooks/PPP2R1A/PPP2R1A.ipynb b/notebooks/PPP2R1A/PPP2R1A.ipynb
@@ -380,7 +380,7 @@
     "\n",
     "txc_service = VVTranscriptCoordinateService(genome_build=GRCh38)\n",
     "tx_coordinates = txc_service.fetch(PPP2R1A_transcript_id)\n",
-    "protein_id = 'NP_037407.4' \n",
+    "protein_id = 'NP_037407.4'\n",
     "\n",
     "pms = UniprotProteinMetadataService()\n",
     "protein_meta = pms.annotate(PPP2R1A_protein_id)"
@@ -420,8 +420,7 @@
     "analysis_config = CohortAnalysisConfiguration()\n",
     "analysis_config.missing_implies_excluded = True\n",
     "analysis_config.pval_correction = 'fdr_bh'\n",
-    "analysis_config.min_perc_patients_w_hpo = 0.1\n",
-    "analysis_config.heuristic_strategy()\n",
+    "analysis_config.heuristic_strategy(threshold_HPO_observed_frequency=0.25)\n",
     "analysis = configure_cohort_analysis(cohort, hpo, config=analysis_config)"
    ]
   },