updated notebooks

pughlab · Oct 5, 2021 · b0d9c86 · b0d9c86
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Showing 14 changed files with 1,875 additions and 8,771 deletions.
diff --git a/notebooks/01_cleanup_CBTTC_manifest.ipynb b/notebooks/01_cleanup_CBTTC_manifest.ipynb
diff --git a/notebooks/02_Master_manifest.ipynb b/notebooks/02_Master_manifest.ipynb
diff --git a/notebooks/03_exp_matrix_4ESTIMATE.ipynb b/notebooks/03_exp_matrix_4ESTIMATE.ipynb
diff --git a/notebooks/04_ESTIMATE_dataframe.ipynb b/notebooks/04_ESTIMATE_dataframe.ipynb
diff --git a/notebooks/05_Cohort_cleanup.ipynb b/notebooks/05_Cohort_cleanup.ipynb
@@ -229,7 +229,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 17,
+   "execution_count": 16,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -248,7 +248,7 @@
   },
   {
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-   "execution_count": 18,
+   "execution_count": 17,
    "metadata": {},
    "outputs": [],
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@@ -264,7 +264,7 @@
   },
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-   "execution_count": 19,
+   "execution_count": 18,
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    "outputs": [],
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@@ -280,7 +280,7 @@
   },
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-   "execution_count": 20,
+   "execution_count": 19,
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@@ -298,7 +298,7 @@
   },
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-   "execution_count": 21,
+   "execution_count": 20,
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@@ -314,7 +314,7 @@
   },
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-   "execution_count": 22,
+   "execution_count": 21,
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@@ -331,7 +331,7 @@
   },
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-   "execution_count": 23,
+   "execution_count": 22,
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@@ -347,7 +347,7 @@
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-   "execution_count": 24,
+   "execution_count": 23,
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@@ -364,7 +364,7 @@
   },
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-   "execution_count": 25,
+   "execution_count": 24,
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@@ -380,7 +380,7 @@
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-   "execution_count": 26,
+   "execution_count": 25,
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@@ -389,7 +389,7 @@
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-   "execution_count": 27,
+   "execution_count": 26,
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@@ -406,7 +406,7 @@
   },
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-   "execution_count": 28,
+   "execution_count": 27,
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@@ -428,7 +428,7 @@
   },
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-   "execution_count": 29,
+   "execution_count": 28,
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@@ -444,7 +444,7 @@
   },
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-   "execution_count": 30,
+   "execution_count": 29,
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@@ -460,7 +460,7 @@
   },
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-   "execution_count": 31,
+   "execution_count": 30,
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@@ -488,7 +488,7 @@
   },
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-   "execution_count": 32,
+   "execution_count": 31,
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@@ -507,7 +507,7 @@
   },
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-   "execution_count": 33,
+   "execution_count": 32,
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     {
@@ -530,7 +530,7 @@
   },
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-   "execution_count": 34,
+   "execution_count": 33,
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@@ -542,7 +542,7 @@
   },
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-   "execution_count": 35,
+   "execution_count": 34,
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     {
@@ -572,7 +572,7 @@
   },
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-   "execution_count": 36,
+   "execution_count": 35,
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@@ -582,7 +582,7 @@
   },
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-   "execution_count": 37,
+   "execution_count": 36,
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     {
@@ -603,7 +603,7 @@
   },
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-   "execution_count": 38,
+   "execution_count": 37,
    "metadata": {},
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     {
@@ -642,7 +642,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 39,
+   "execution_count": 38,
    "metadata": {},
    "outputs": [
     {
@@ -661,9 +661,26 @@
     "table(estimate_manifest_primary_clean$group)"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Replace CBTTC with CBTN and DKFZ with ICGC"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 39,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "estimate_manifest_primary_clean$group[estimate_manifest_primary_clean$group == \"DKFZ\"] <- \"ICGC\"\n",
+    "estimate_manifest_primary_clean$group[estimate_manifest_primary_clean$group == \"CBTTC\"] <- \"CBTN\""
+   ]
+  },
   {
    "cell_type": "code",
-   "execution_count": 41,
+   "execution_count": 40,
    "metadata": {},
    "outputs": [],
    "source": [