few updates

pughlab · Oct 14, 2021 · 811e718 · 811e718
1 parent e05777b
commit 811e718
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Showing 11 changed files with 3,194 additions and 4,268 deletions.
diff --git a/notebooks/02_Master_manifest.ipynb b/notebooks/02_Master_manifest.ipynb
diff --git a/notebooks/04_ESTIMATE_dataframe.ipynb b/notebooks/04_ESTIMATE_dataframe.ipynb
@@ -128,23 +128,23 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 5,
+   "execution_count": 6,
    "metadata": {},
    "outputs": [
     {
      "data": {
       "text/plain": [
        "\n",
-       "   0    1 \n",
-       "2029 2407 "
+       " CBTTC   DKFZ TARGET   TCGA \n",
+       "   969    199    157   3204 "
       ]
      },
      "metadata": {},
      "output_type": "display_data"
     }
    ],
    "source": [
-    "table(IPD_metadata$vital_status)"
+    "table(IPD_metadata$group)"
    ]
   },
   {
@@ -170,7 +170,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 6,
+   "execution_count": 7,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -180,7 +180,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 7,
+   "execution_count": 8,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -196,7 +196,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 8,
+   "execution_count": 9,
    "metadata": {},
    "outputs": [
     {
@@ -708,7 +708,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 9,
+   "execution_count": 10,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -733,7 +733,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 10,
+   "execution_count": 11,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -749,7 +749,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 11,
+   "execution_count": 12,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -760,7 +760,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 12,
+   "execution_count": 13,
    "metadata": {},
    "outputs": [
     {
@@ -799,7 +799,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 13,
+   "execution_count": 14,
    "metadata": {},
    "outputs": [
     {
@@ -869,7 +869,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 14,
+   "execution_count": 15,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -878,7 +878,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 15,
+   "execution_count": 16,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -888,7 +888,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 16,
+   "execution_count": 17,
    "metadata": {},
    "outputs": [
     {
@@ -965,7 +965,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 17,
+   "execution_count": 18,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -986,7 +986,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 18,
+   "execution_count": 17,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -995,7 +995,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 19,
+   "execution_count": 18,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -1004,7 +1004,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 20,
+   "execution_count": 19,
    "metadata": {},
    "outputs": [
     {
@@ -1032,7 +1032,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 21,
+   "execution_count": 20,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -1048,7 +1048,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 22,
+   "execution_count": 21,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -1057,7 +1057,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 23,
+   "execution_count": 22,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -1080,7 +1080,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 24,
+   "execution_count": 23,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -1097,7 +1097,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 25,
+   "execution_count": 24,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -1107,7 +1107,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 26,
+   "execution_count": 25,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -1117,7 +1117,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 27,
+   "execution_count": 26,
    "metadata": {},
    "outputs": [
     {
@@ -1156,7 +1156,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 28,
+   "execution_count": 27,
    "metadata": {},
    "outputs": [
     {
@@ -1177,23 +1177,23 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 29,
+   "execution_count": 28,
    "metadata": {},
    "outputs": [
     {
      "data": {
       "text/plain": [
        "\n",
-       "   0    1 \n",
-       "1585 1860 "
+       " CBTTC   DKFZ TARGET   TCGA \n",
+       "   730    196    149   2452 "
       ]
      },
      "metadata": {},
      "output_type": "display_data"
     }
    ],
    "source": [
-    "table(estimate_manifest_primary$vital_status)"
+    "table(estimate_manifest_primary$group)"
    ]
   },
   {
@@ -1215,6 +1215,13 @@
     "save(PDX_estimate,\n",
     "     file = paste0(datapath, \"ESTIMATE/PDX_estimate.RData\"))   "
    ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
   }
  ],
  "metadata": {

diff --git a/notebooks/05_Cohort_cleanup.ipynb b/notebooks/05_Cohort_cleanup.ipynb
@@ -680,7 +680,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 41,
+   "execution_count": 40,
    "metadata": {},
    "outputs": [],
    "source": [