diff --git a/interactomes/PCNet.05_2018.oi2 b/interactomes/PCNet.05_2018.oi2
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+oid sha256:18bba1b9612ffde9b729deac04216a666da50c8ac4571e7726cd6bb9ca406d41
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diff --git a/interactomes/PreProcess_PCNet_For_OmicsIntegrator.ipynb b/interactomes/PreProcess_PCNet_For_OmicsIntegrator.ipynb
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+{
+ "cells": [
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "# PreProcessing PCNet for OmicsIntegrator\n",
+ "\n",
+ "All Fraenkel-lab interactomes have been pre-processed to have 3 columns: 2 interactors and a scalar confidence\n",
+ "However, OmicsIntegrator requires that edges have a cost, not a confidence. This notebook sets costs on the edges and augments those interactomes for use in OmicsIntegrator."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 1,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "import numpy as np\n",
+ "import pandas as pd\n",
+ "import matplotlib.pyplot as plt\n",
+ "%matplotlib inline"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 2,
+ "metadata": {},
+ "outputs": [
+ {
+ "data": {
+ "text/html": [
+ "
\n",
+ "\n",
+ "
\n",
+ " \n",
+ " \n",
+ " | \n",
+ " protein1 | \n",
+ " protein2 | \n",
+ " confidence | \n",
+ "
\n",
+ " \n",
+ " \n",
+ " \n",
+ " 0 | \n",
+ " A1BG | \n",
+ " A2M | \n",
+ " NaN | \n",
+ "
\n",
+ " \n",
+ " 1 | \n",
+ " A1BG | \n",
+ " ABCC6 | \n",
+ " NaN | \n",
+ "
\n",
+ " \n",
+ " 2 | \n",
+ " A1BG | \n",
+ " ACOT12 | \n",
+ " NaN | \n",
+ "
\n",
+ " \n",
+ " 3 | \n",
+ " A1BG | \n",
+ " ADH1A | \n",
+ " NaN | \n",
+ "
\n",
+ " \n",
+ " 4 | \n",
+ " A1BG | \n",
+ " ADH4 | \n",
+ " NaN | \n",
+ "
\n",
+ " \n",
+ "
\n",
+ "
"
+ ],
+ "text/plain": [
+ " protein1 protein2 confidence\n",
+ "0 A1BG A2M NaN\n",
+ "1 A1BG ABCC6 NaN\n",
+ "2 A1BG ACOT12 NaN\n",
+ "3 A1BG ADH1A NaN\n",
+ "4 A1BG ADH4 NaN"
+ ]
+ },
+ "execution_count": 2,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "pcnet = pd.read_pickle(\"../../interactomes/PCNet/PCNet.05_2018.cleaned.namespace-mapped.full.pickle\")\n",
+ "pcnet.head()"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "### PCNet is relatively unique in that we don't have confidences for the edges. We'll need to set them arbitrarily"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 3,
+ "metadata": {},
+ "outputs": [
+ {
+ "data": {
+ "text/html": [
+ "\n",
+ "\n",
+ "
\n",
+ " \n",
+ " \n",
+ " | \n",
+ " protein1 | \n",
+ " protein2 | \n",
+ " cost | \n",
+ "
\n",
+ " \n",
+ " \n",
+ " \n",
+ " 0 | \n",
+ " A1BG | \n",
+ " A2M | \n",
+ " 1.0 | \n",
+ "
\n",
+ " \n",
+ " 1 | \n",
+ " A1BG | \n",
+ " ABCC6 | \n",
+ " 1.0 | \n",
+ "
\n",
+ " \n",
+ " 2 | \n",
+ " A1BG | \n",
+ " ACOT12 | \n",
+ " 1.0 | \n",
+ "
\n",
+ " \n",
+ " 3 | \n",
+ " A1BG | \n",
+ " ADH1A | \n",
+ " 1.0 | \n",
+ "
\n",
+ " \n",
+ " 4 | \n",
+ " A1BG | \n",
+ " ADH4 | \n",
+ " 1.0 | \n",
+ "
\n",
+ " \n",
+ "
\n",
+ "
"
+ ],
+ "text/plain": [
+ " protein1 protein2 cost\n",
+ "0 A1BG A2M 1.0\n",
+ "1 A1BG ABCC6 1.0\n",
+ "2 A1BG ACOT12 1.0\n",
+ "3 A1BG ADH1A 1.0\n",
+ "4 A1BG ADH4 1.0"
+ ]
+ },
+ "execution_count": 3,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "pcnet['cost'] = 1.0\n",
+ "del pcnet['confidence']\n",
+ "\n",
+ "pcnet.head()"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 4,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "pcnet.to_csv('PCNet.05_2018.oi2', sep='\\t', index=False)\n"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": []
+ }
+ ],
+ "metadata": {
+ "kernelspec": {
+ "display_name": "Python 3",
+ "language": "python",
+ "name": "python3"
+ },
+ "language_info": {
+ "codemirror_mode": {
+ "name": "ipython",
+ "version": 3
+ },
+ "file_extension": ".py",
+ "mimetype": "text/x-python",
+ "name": "python",
+ "nbconvert_exporter": "python",
+ "pygments_lexer": "ipython3",
+ "version": "3.6.5"
+ }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}