Improve documentation for PIP cutoff

code/mnm_analysis/mnm_regression.ipynb

@@ -509,8 +509,9 @@
     "parameter: indel = True\n",
     "parameter: pip_cutoff = 0.025\n",
     "parameter: coverage = [0.95, 0.7, 0.5]\n",
-    "# If this value is greater than 0, an initial single effect analysis will be performed \n",
+    "# If this value is not 0, then an initial single effect analysis will be performed \n",
     "# to determine if follow up analysis will be continued or to simply return NULL\n",
+    "# If this is negative we use a default way to determine this cutoff which is conservative but still useful\n",
     "parameter: skip_analysis_pip_cutoff = []\n",
     "# Skip fine-mapping\n",
     "parameter: skip_fine_mapping = False\n",
@@ -547,7 +548,7 @@
     "    raise ValueError(\"Number of input phenotypes files must match the number of phenotype ID mapping files\")\n",
     "\n",
     "if len(skip_analysis_pip_cutoff) == 0:\n",
-    "    skip_analysis_pip_cutoff = [-1.0] * len(phenoFile)\n",
+    "    skip_analysis_pip_cutoff = [0.0] * len(phenoFile)\n",
     "if len(skip_analysis_pip_cutoff) == 1:\n",
     "    skip_analysis_pip_cutoff = skip_analysis_pip_cutoff * len(phenoFile)\n",
     "if len(skip_analysis_pip_cutoff) != len(phenoFile):\n",
@@ -1211,7 +1212,7 @@
     "    genes = [genes]\n",
     "\n",
     "if len(skip_analysis_pip_cutoff) == 0:\n",
-    "    skip_analysis_pip_cutoff = [-1.0] * len(genes)\n",
+    "    skip_analysis_pip_cutoff = [0.0] * len(genes)\n",
     "\n",
     "if len(skip_analysis_pip_cutoff) == 1:\n",
     "    skip_analysis_pip_cutoff = skip_analysis_pip_cutoff * len(genes)\n",