Example.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "from pandas_plink import read_plink\n",
    "(bim, fam, bed) = read_plink('pandas_plink/test/data_files/chr*', verbose=False)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
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       "\n",
       "    .dataframe tbody tr th {\n",
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       "    }\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>chrom</th>\n",
       "      <th>snp</th>\n",
       "      <th>cm</th>\n",
       "      <th>pos</th>\n",
       "      <th>a0</th>\n",
       "      <th>a1</th>\n",
       "      <th>i</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>11</td>\n",
       "      <td>316849996</td>\n",
       "      <td>0.0</td>\n",
       "      <td>157439</td>\n",
       "      <td>C</td>\n",
       "      <td>T</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>11</td>\n",
       "      <td>316874359</td>\n",
       "      <td>0.0</td>\n",
       "      <td>181802</td>\n",
       "      <td>G</td>\n",
       "      <td>C</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>11</td>\n",
       "      <td>316941526</td>\n",
       "      <td>0.0</td>\n",
       "      <td>248969</td>\n",
       "      <td>G</td>\n",
       "      <td>C</td>\n",
       "      <td>2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>11</td>\n",
       "      <td>317137620</td>\n",
       "      <td>0.0</td>\n",
       "      <td>445063</td>\n",
       "      <td>C</td>\n",
       "      <td>T</td>\n",
       "      <td>3</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>11</td>\n",
       "      <td>317534352</td>\n",
       "      <td>0.0</td>\n",
       "      <td>841795</td>\n",
       "      <td>C</td>\n",
       "      <td>T</td>\n",
       "      <td>4</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "  chrom        snp   cm     pos a0 a1  i\n",
       "0    11  316849996  0.0  157439  C  T  0\n",
       "1    11  316874359  0.0  181802  G  C  1\n",
       "2    11  316941526  0.0  248969  G  C  2\n",
       "3    11  317137620  0.0  445063  C  T  3\n",
       "4    11  317534352  0.0  841795  C  T  4"
      ]
     },
     "execution_count": 2,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "bim.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
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       "\n",
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       "    }\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>fid</th>\n",
       "      <th>iid</th>\n",
       "      <th>father</th>\n",
       "      <th>mother</th>\n",
       "      <th>gender</th>\n",
       "      <th>trait</th>\n",
       "      <th>i</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>B001</td>\n",
       "      <td>B001</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>-9</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>B002</td>\n",
       "      <td>B002</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>-9</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>B003</td>\n",
       "      <td>B003</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>-9</td>\n",
       "      <td>2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>B004</td>\n",
       "      <td>B004</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>-9</td>\n",
       "      <td>3</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>B005</td>\n",
       "      <td>B005</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>-9</td>\n",
       "      <td>4</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "    fid   iid father mother gender trait  i\n",
       "0  B001  B001      0      0      0    -9  0\n",
       "1  B002  B002      0      0      0    -9  1\n",
       "2  B003  B003      0      0      0    -9  2\n",
       "3  B004  B004      0      0      0    -9  3\n",
       "4  B005  B005      0      0      0    -9  4"
      ]
     },
     "execution_count": 3,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "fam.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
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       "  </thead>\n",
       "  <tbody>\n",
       "    <tr><th> Bytes </th><td> 70.11 kB </td> <td> 43.62 kB </td></tr>\n",
       "    <tr><th> Shape </th><td> (1252, 14) </td> <td> (779, 14) </td></tr>\n",
       "    <tr><th> Count </th><td> 6 Tasks </td><td> 2 Chunks </td></tr>\n",
       "    <tr><th> Type </th><td> float32 </td><td> numpy.ndarray </td></tr>\n",
       "  </tbody>\n",
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      ],
      "text/plain": [
       "dask.array<concatenate, shape=(1252, 14), dtype=float32, chunksize=(779, 14), chunktype=numpy.ndarray>"
      ]
     },
     "execution_count": 4,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "bed"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "    }\n",
       "\n",
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       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>chrom</th>\n",
       "      <th>snp</th>\n",
       "      <th>cm</th>\n",
       "      <th>pos</th>\n",
       "      <th>a0</th>\n",
       "      <th>a1</th>\n",
       "      <th>i</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>11</td>\n",
       "      <td>316849996</td>\n",
       "      <td>0.0</td>\n",
       "      <td>157439</td>\n",
       "      <td>C</td>\n",
       "      <td>T</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>11</td>\n",
       "      <td>316874359</td>\n",
       "      <td>0.0</td>\n",
       "      <td>181802</td>\n",
       "      <td>G</td>\n",
       "      <td>C</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>11</td>\n",
       "      <td>316941526</td>\n",
       "      <td>0.0</td>\n",
       "      <td>248969</td>\n",
       "      <td>G</td>\n",
       "      <td>C</td>\n",
       "      <td>2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>11</td>\n",
       "      <td>317137620</td>\n",
       "      <td>0.0</td>\n",
       "      <td>445063</td>\n",
       "      <td>C</td>\n",
       "      <td>T</td>\n",
       "      <td>3</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>11</td>\n",
       "      <td>317534352</td>\n",
       "      <td>0.0</td>\n",
       "      <td>841795</td>\n",
       "      <td>C</td>\n",
       "      <td>T</td>\n",
       "      <td>4</td>\n",
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       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "  chrom        snp   cm     pos a0 a1  i\n",
       "0    11  316849996  0.0  157439  C  T  0\n",
       "1    11  316874359  0.0  181802  G  C  1\n",
       "2    11  316941526  0.0  248969  G  C  2\n",
       "3    11  317137620  0.0  445063  C  T  3\n",
       "4    11  317534352  0.0  841795  C  T  4"
      ]
     },
     "execution_count": 5,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "chrom11 = bim[bim[\"chrom\"] == \"11\"]\n",
    "chrom11.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [],
   "source": [
    "window = 50000\n",
    "center = 18908037\n",
    "left = center - window\n",
    "right = center + window\n",
    "\n",
    "chrom11 = chrom11.reset_index()\n",
    "i = chrom11[(chrom11['pos'] > left) & (chrom11['pos'] < right)].i"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "array([[ 0.,  0.,  0.,  0.,  0.,  2.,  2.,  0.,  2.,  2.,  2.,  2.,  2.,\n",
       "         0.],\n",
       "       [ 0., nan,  0.,  0.,  0.,  2., nan,  0.,  2.,  2.,  2.,  2.,  2.,\n",
       "         0.],\n",
       "       [nan,  0.,  0.,  0.,  0.,  2.,  2.,  0.,  2.,  2.,  2.,  1.,  1.,\n",
       "        nan],\n",
       "       [ 0.,  0.,  0.,  0.,  0.,  2.,  2.,  0.,  2.,  2.,  2.,  2.,  2.,\n",
       "         0.],\n",
       "       [ 0.,  0.,  0.,  0.,  0.,  2.,  2.,  0.,  2.,  2.,  2.,  2.,  2.,\n",
       "         0.],\n",
       "       [nan,  2.,  2.,  2.,  2.,  0.,  0., nan,  0.,  0.,  0.,  1.,  1.,\n",
       "         2.],\n",
       "       [ 0.,  0.,  0.,  0.,  0.,  2.,  2.,  0.,  2.,  2.,  2.,  2.,  2.,\n",
       "         0.],\n",
       "       [ 0.,  0.,  0.,  0.,  0.,  2.,  2.,  0.,  2.,  2.,  2.,  2.,  2.,\n",
       "         0.]], dtype=float32)"
      ]
     },
     "execution_count": 7,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# Display dosage of allele a1 (by definition)\n",
    "# NaN values mean missing values\n",
    "X = bed[i.values, :].compute()\n",
    "X"
   ]
  }
 ],
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