From 948f30141804fcf1e0445e60bc709f48c3080b54 Mon Sep 17 00:00:00 2001 From: aakan96 <aakan96@mi.fu-berlin.de> Date: Fri, 21 Jul 2023 12:31:47 +0000 Subject: [PATCH] Update file mRNA_limma_dataset_svm_final.ipynb --- .../mRNA_limma_dataset_svm_final.ipynb | 416 +----------------- 1 file changed, 22 insertions(+), 394 deletions(-) diff --git a/03_Machine_Learning/mRNA_limma_dataset_svm_final.ipynb b/03_Machine_Learning/mRNA_limma_dataset_svm_final.ipynb index 950334d..46d1177 100644 --- a/03_Machine_Learning/mRNA_limma_dataset_svm_final.ipynb +++ b/03_Machine_Learning/mRNA_limma_dataset_svm_final.ipynb @@ -388,379 +388,7 @@ }, { "cell_type": "code", - "execution_count": 33, - "id": "f0f1977f", - "metadata": {}, - "outputs": [ - { - "data": { - "text/html": [ - "<div>\n", - "<style scoped>\n", - " .dataframe tbody tr th:only-of-type {\n", - " vertical-align: middle;\n", - " }\n", - "\n", - " .dataframe tbody tr th {\n", - " vertical-align: top;\n", - " }\n", - "\n", - " .dataframe thead th {\n", - " text-align: right;\n", - " }\n", - "</style>\n", - "<table border=\"1\" class=\"dataframe\">\n", - " <thead>\n", - " <tr style=\"text-align: right;\">\n", - " <th></th>\n", - " <th>ABAT</th>\n", - " <th>ABHD5</th>\n", - " <th>ABLIM1</th>\n", - " <th>ABLIM3</th>\n", - " <th>ACAA1</th>\n", - " <th>ACADM</th>\n", - " <th>ACADVL</th>\n", - " <th>ACD</th>\n", - " <th>ACLY</th>\n", - " <th>ACOT11</th>\n", - " <th>...</th>\n", - " <th>XYLT1</th>\n", - " <th>YOD1</th>\n", - " <th>YTHDC1</th>\n", - " <th>ZBTB16</th>\n", - " <th>ZDHHC13</th>\n", - " <th>ZFP64</th>\n", - " <th>ZNF185</th>\n", - " <th>ZNF365</th>\n", - " <th>ZNF426</th>\n", - " <th>ZNF710</th>\n", - " </tr>\n", - " </thead>\n", - " <tbody>\n", - " <tr>\n", - " <th>0</th>\n", - " <td>186</td>\n", - " <td>2603</td>\n", - " <td>42653</td>\n", - " <td>220</td>\n", - " <td>2132</td>\n", - " <td>22869</td>\n", - " <td>19775</td>\n", - " <td>4486</td>\n", - " <td>8835</td>\n", - " <td>2332</td>\n", - " <td>...</td>\n", - " <td>392</td>\n", - " <td>222</td>\n", - " <td>295</td>\n", - " <td>4598</td>\n", - " <td>7009</td>\n", - " <td>568</td>\n", - " <td>65123</td>\n", - " <td>56</td>\n", - " <td>308</td>\n", - " <td>10385</td>\n", - " </tr>\n", - " <tr>\n", - " <th>1</th>\n", - " <td>93</td>\n", - " <td>1137</td>\n", - " <td>16493</td>\n", - " <td>69</td>\n", - " <td>1816</td>\n", - " <td>17788</td>\n", - " <td>16870</td>\n", - " <td>7993</td>\n", - " <td>21434</td>\n", - " <td>2211</td>\n", - " <td>...</td>\n", - " <td>62</td>\n", - " <td>78</td>\n", - " <td>144</td>\n", - " <td>2132</td>\n", - " <td>2602</td>\n", - " <td>1720</td>\n", - " <td>13531</td>\n", - " <td>47</td>\n", - " <td>140</td>\n", - " <td>6441</td>\n", - " </tr>\n", - " <tr>\n", - " <th>2</th>\n", - " <td>198</td>\n", - " <td>5593</td>\n", - " <td>53918</td>\n", - " <td>263</td>\n", - " <td>3490</td>\n", - " <td>39276</td>\n", - " <td>25847</td>\n", - " <td>4413</td>\n", - " <td>9212</td>\n", - " <td>7419</td>\n", - " <td>...</td>\n", - " <td>481</td>\n", - " <td>355</td>\n", - " <td>308</td>\n", - " <td>1071</td>\n", - " <td>10289</td>\n", - " <td>379</td>\n", - " <td>65131</td>\n", - " <td>206</td>\n", - " <td>1251</td>\n", - " <td>11768</td>\n", - " </tr>\n", - " <tr>\n", - " <th>3</th>\n", - " <td>104</td>\n", - " <td>1636</td>\n", - " <td>19203</td>\n", - " <td>127</td>\n", - " <td>1518</td>\n", - " <td>17951</td>\n", - " <td>16854</td>\n", - " <td>12800</td>\n", - " <td>11939</td>\n", - " <td>5136</td>\n", - " <td>...</td>\n", - " <td>213</td>\n", - " <td>122</td>\n", - " <td>244</td>\n", - " <td>482</td>\n", - " <td>3578</td>\n", - " <td>1990</td>\n", - " <td>37715</td>\n", - " <td>66</td>\n", - " <td>361</td>\n", - " <td>8517</td>\n", - " </tr>\n", - " <tr>\n", - " <th>4</th>\n", - " <td>205</td>\n", - " <td>4720</td>\n", - " <td>56984</td>\n", - " <td>495</td>\n", - " <td>3309</td>\n", - " <td>24427</td>\n", - " <td>28197</td>\n", - " <td>5718</td>\n", - " <td>8192</td>\n", - " <td>6748</td>\n", - " <td>...</td>\n", - " <td>169</td>\n", - " <td>275</td>\n", - " <td>200</td>\n", - " <td>3632</td>\n", - " <td>7275</td>\n", - " <td>509</td>\n", - " <td>65138</td>\n", - " <td>188</td>\n", - " <td>587</td>\n", - " <td>9390</td>\n", - " </tr>\n", - " <tr>\n", - " <th>...</th>\n", - " <td>...</td>\n", - " <td>...</td>\n", - " <td>...</td>\n", - " <td>...</td>\n", - " <td>...</td>\n", - " <td>...</td>\n", - " <td>...</td>\n", - " <td>...</td>\n", - " <td>...</td>\n", - " <td>...</td>\n", - " <td>...</td>\n", - " <td>...</td>\n", - " <td>...</td>\n", - " <td>...</td>\n", - " <td>...</td>\n", - " <td>...</td>\n", - " <td>...</td>\n", - " <td>...</td>\n", - " <td>...</td>\n", - " <td>...</td>\n", - " <td>...</td>\n", - " </tr>\n", - " <tr>\n", - " <th>214</th>\n", - " <td>4</td>\n", - " <td>5</td>\n", - " <td>9</td>\n", - " <td>6</td>\n", - " <td>7</td>\n", - " <td>7</td>\n", - " <td>10</td>\n", - " <td>8</td>\n", - " <td>7</td>\n", - " <td>7</td>\n", - " <td>...</td>\n", - " <td>7</td>\n", - " <td>4</td>\n", - " <td>9</td>\n", - " <td>6</td>\n", - " <td>7</td>\n", - " <td>7</td>\n", - " <td>7</td>\n", - " <td>6</td>\n", - " <td>5</td>\n", - " <td>8</td>\n", - " </tr>\n", - " <tr>\n", - " <th>215</th>\n", - " <td>5</td>\n", - " <td>5</td>\n", - " <td>8</td>\n", - " <td>8</td>\n", - " <td>8</td>\n", - " <td>8</td>\n", - " <td>9</td>\n", - " <td>8</td>\n", - " <td>6</td>\n", - " <td>7</td>\n", - " <td>...</td>\n", - " <td>7</td>\n", - " <td>4</td>\n", - " <td>9</td>\n", - " <td>6</td>\n", - " <td>6</td>\n", - " <td>7</td>\n", - " <td>9</td>\n", - " <td>6</td>\n", - " <td>5</td>\n", - " <td>8</td>\n", - " </tr>\n", - " <tr>\n", - " <th>216</th>\n", - " <td>4</td>\n", - " <td>5</td>\n", - " <td>9</td>\n", - " <td>6</td>\n", - " <td>7</td>\n", - " <td>8</td>\n", - " <td>9</td>\n", - " <td>8</td>\n", - " <td>7</td>\n", - " <td>7</td>\n", - " <td>...</td>\n", - " <td>7</td>\n", - " <td>5</td>\n", - " <td>9</td>\n", - " <td>6</td>\n", - " <td>6</td>\n", - " <td>7</td>\n", - " <td>8</td>\n", - " <td>6</td>\n", - " <td>5</td>\n", - " <td>8</td>\n", - " </tr>\n", - " <tr>\n", - " <th>217</th>\n", - " <td>5</td>\n", - " <td>4</td>\n", - " <td>9</td>\n", - " <td>7</td>\n", - " <td>8</td>\n", - " <td>8</td>\n", - " <td>9</td>\n", - " <td>8</td>\n", - " <td>6</td>\n", - " <td>7</td>\n", - " <td>...</td>\n", - " <td>7</td>\n", - " <td>4</td>\n", - " <td>10</td>\n", - " <td>6</td>\n", - " <td>8</td>\n", - " <td>7</td>\n", - " <td>8</td>\n", - " <td>6</td>\n", - " <td>5</td>\n", - " <td>8</td>\n", - " </tr>\n", - " <tr>\n", - " <th>218</th>\n", - " <td>4</td>\n", - " <td>4</td>\n", - " <td>7</td>\n", - " <td>6</td>\n", - " <td>8</td>\n", - " <td>8</td>\n", - " <td>10</td>\n", - " <td>8</td>\n", - " <td>7</td>\n", - " <td>7</td>\n", - " <td>...</td>\n", - " <td>6</td>\n", - " <td>5</td>\n", - " <td>10</td>\n", - " <td>6</td>\n", - " <td>6</td>\n", - " <td>7</td>\n", - " <td>6</td>\n", - " <td>5</td>\n", - " <td>5</td>\n", - " <td>8</td>\n", - " </tr>\n", - " </tbody>\n", - "</table>\n", - "<p>219 rows × 578 columns</p>\n", - "</div>" - ], - "text/plain": [ - " ABAT ABHD5 ABLIM1 ABLIM3 ACAA1 ACADM ACADVL ACD ACLY ACOT11 \\\n", - "0 186 2603 42653 220 2132 22869 19775 4486 8835 2332 \n", - "1 93 1137 16493 69 1816 17788 16870 7993 21434 2211 \n", - "2 198 5593 53918 263 3490 39276 25847 4413 9212 7419 \n", - "3 104 1636 19203 127 1518 17951 16854 12800 11939 5136 \n", - "4 205 4720 56984 495 3309 24427 28197 5718 8192 6748 \n", - ".. ... ... ... ... ... ... ... ... ... ... \n", - "214 4 5 9 6 7 7 10 8 7 7 \n", - "215 5 5 8 8 8 8 9 8 6 7 \n", - "216 4 5 9 6 7 8 9 8 7 7 \n", - "217 5 4 9 7 8 8 9 8 6 7 \n", - "218 4 4 7 6 8 8 10 8 7 7 \n", - "\n", - " ... XYLT1 YOD1 YTHDC1 ZBTB16 ZDHHC13 ZFP64 ZNF185 ZNF365 ZNF426 \\\n", - "0 ... 392 222 295 4598 7009 568 65123 56 308 \n", - "1 ... 62 78 144 2132 2602 1720 13531 47 140 \n", - "2 ... 481 355 308 1071 10289 379 65131 206 1251 \n", - "3 ... 213 122 244 482 3578 1990 37715 66 361 \n", - "4 ... 169 275 200 3632 7275 509 65138 188 587 \n", - ".. ... ... ... ... ... ... ... ... ... ... \n", - "214 ... 7 4 9 6 7 7 7 6 5 \n", - "215 ... 7 4 9 6 6 7 9 6 5 \n", - "216 ... 7 5 9 6 6 7 8 6 5 \n", - "217 ... 7 4 10 6 8 7 8 6 5 \n", - "218 ... 6 5 10 6 6 7 6 5 5 \n", - "\n", - " ZNF710 \n", - "0 10385 \n", - "1 6441 \n", - "2 11768 \n", - "3 8517 \n", - "4 9390 \n", - ".. ... \n", - "214 8 \n", - "215 8 \n", - "216 8 \n", - "217 8 \n", - "218 8 \n", - "\n", - "[219 rows x 578 columns]" - ] - }, - "execution_count": 33, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "X" - ] - }, - { - "cell_type": "code", - "execution_count": 34, + "execution_count": null, "id": "1cc528fb", "metadata": {}, "outputs": [], @@ -781,7 +409,7 @@ }, { "cell_type": "code", - "execution_count": 35, + "execution_count": null, "id": "8afa29ae", "metadata": {}, "outputs": [ @@ -810,7 +438,7 @@ }, { "cell_type": "code", - "execution_count": 36, + "execution_count": null, "id": "3af09ef8", "metadata": {}, "outputs": [], @@ -821,7 +449,7 @@ }, { "cell_type": "code", - "execution_count": 37, + "execution_count": null, "id": "129430e6", "metadata": {}, "outputs": [ @@ -857,7 +485,7 @@ }, { "cell_type": "code", - "execution_count": 38, + "execution_count": null, "id": "1fbca4b8", "metadata": {}, "outputs": [], @@ -869,7 +497,7 @@ }, { "cell_type": "code", - "execution_count": 39, + "execution_count": null, "id": "0502e118", "metadata": {}, "outputs": [], @@ -883,7 +511,7 @@ }, { "cell_type": "code", - "execution_count": 40, + "execution_count": null, "id": "7f2d18b0", "metadata": {}, "outputs": [], @@ -894,7 +522,7 @@ }, { "cell_type": "code", - "execution_count": 41, + "execution_count": null, "id": "79790f1d", "metadata": {}, "outputs": [ @@ -957,7 +585,7 @@ }, { "cell_type": "code", - "execution_count": 42, + "execution_count": null, "id": "5d327876", "metadata": {}, "outputs": [ @@ -980,7 +608,7 @@ }, { "cell_type": "code", - "execution_count": 43, + "execution_count": null, "id": "f8d67e2f", "metadata": {}, "outputs": [], @@ -991,7 +619,7 @@ }, { "cell_type": "code", - "execution_count": 44, + "execution_count": null, "id": "3b2776c0", "metadata": {}, "outputs": [ @@ -1016,7 +644,7 @@ }, { "cell_type": "code", - "execution_count": 45, + "execution_count": null, "id": "94871ada", "metadata": {}, "outputs": [], @@ -1026,7 +654,7 @@ }, { "cell_type": "code", - "execution_count": 46, + "execution_count": null, "id": "f8d4142d", "metadata": {}, "outputs": [ @@ -1064,7 +692,7 @@ }, { "cell_type": "code", - "execution_count": 57, + "execution_count": null, "id": "6b5692ba", "metadata": {}, "outputs": [ @@ -1104,7 +732,7 @@ }, { "cell_type": "code", - "execution_count": 47, + "execution_count": null, "id": "a85470f6", "metadata": {}, "outputs": [ @@ -1132,7 +760,7 @@ }, { "cell_type": "code", - "execution_count": 48, + "execution_count": null, "id": "f7247260", "metadata": {}, "outputs": [ @@ -1159,7 +787,7 @@ }, { "cell_type": "code", - "execution_count": 49, + "execution_count": null, "id": "475b75bd", "metadata": {}, "outputs": [ @@ -1188,7 +816,7 @@ }, { "cell_type": "code", - "execution_count": 50, + "execution_count": null, "id": "c1095af0", "metadata": {}, "outputs": [], @@ -1202,7 +830,7 @@ }, { "cell_type": "code", - "execution_count": 51, + "execution_count": null, "id": "ae7e0162", "metadata": {}, "outputs": [], @@ -1212,7 +840,7 @@ }, { "cell_type": "code", - "execution_count": 52, + "execution_count": null, "id": "1d97f818", "metadata": {}, "outputs": [], @@ -1222,7 +850,7 @@ }, { "cell_type": "code", - "execution_count": 53, + "execution_count": null, "id": "4cd4227b", "metadata": {}, "outputs": [ @@ -1250,7 +878,7 @@ }, { "cell_type": "code", - "execution_count": 54, + "execution_count": null, "id": "8f6d88bb", "metadata": {}, "outputs": [ -- GitLab