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KaiSmith/genda: Loading and Viewing Data Secret

Last active December 18, 2015 10:29
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IPython Notebook tutorial for using genda: Loading and Viewing Data Viewable at http://nbviewer.ipython.org/af733a3b544548c9b6c6
Raw
genda: Loading and Viewing Data
{
"metadata": {
"name": "genda - Loading and Viewing Data"
},
"nbformat": 2,
"worksheets": [
{
"cells": [
{
"cell_type": "code",
"collapsed": true,
"input": [
"from genda.formats.panVCF import VCF",
"from genda.formats.Snp_array import SNP_array",
"from genda.formats.PED import PED"
],
"language": "python",
"outputs": [],
"prompt_number": 1
},
{
"cell_type": "code",
"collapsed": true,
"input": [
"v = VCF('./tests/data/chr22.test.vcf')"
],
"language": "python",
"outputs": [],
"prompt_number": 2
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"#Preview VCF",
"v.vcf.ix[0:10,0:7]"
],
"language": "python",
"outputs": [
{
"html": [
"<div style=\"max-height:1000px;max-width:1500px;overflow:auto;\">",
"<table border=\"1\" class=\"dataframe\">",
" <thead>",
" <tr style=\"text-align: right;\">",
" <th></th>",
" <th>#CHROM</th>",
" <th>POS</th>",
" <th>REF</th>",
" <th>ALT</th>",
" <th>QUAL</th>",
" <th>FILTER</th>",
" <th>FORMAT</th>",
" </tr>",
" </thead>",
" <tbody>",
" <tr>",
" <th>rs149201999</th>",
" <td> 22</td>",
" <td> 16050408</td>",
" <td> T</td>",
" <td> C</td>",
" <td> 100</td>",
" <td> PASS</td>",
" <td> GT:DS:GL</td>",
" </tr>",
" <tr>",
" <th>rs146752890</th>",
" <td> 22</td>",
" <td> 16050612</td>",
" <td> C</td>",
" <td> G</td>",
" <td> 100</td>",
" <td> PASS</td>",
" <td> GT:DS:GL</td>",
" </tr>",
" <tr>",
" <th>rs139377059</th>",
" <td> 22</td>",
" <td> 16050678</td>",
" <td> C</td>",
" <td> T</td>",
" <td> 100</td>",
" <td> PASS</td>",
" <td> GT:DS:GL</td>",
" </tr>",
" <tr>",
" <th>rs188945759</th>",
" <td> 22</td>",
" <td> 16050984</td>",
" <td> C</td>",
" <td> G</td>",
" <td> 100</td>",
" <td> PASS</td>",
" <td> GT:DS:GL</td>",
" </tr>",
" <tr>",
" <th>rs6518357</th>",
" <td> 22</td>",
" <td> 16051107</td>",
" <td> C</td>",
" <td> A</td>",
" <td> 100</td>",
" <td> PASS</td>",
" <td> GT:DS:GL</td>",
" </tr>",
" <tr>",
" <th>rs62224609</th>",
" <td> 22</td>",
" <td> 16051249</td>",
" <td> T</td>",
" <td> C</td>",
" <td> 100</td>",
" <td> PASS</td>",
" <td> GT:DS:GL</td>",
" </tr>",
" <tr>",
" <th>rs62224610</th>",
" <td> 22</td>",
" <td> 16051347</td>",
" <td> G</td>",
" <td> C</td>",
" <td> 100</td>",
" <td> PASS</td>",
" <td> GT:DS:GL</td>",
" </tr>",
" <tr>",
" <th>rs143503259</th>",
" <td> 22</td>",
" <td> 16051453</td>",
" <td> A</td>",
" <td> C</td>",
" <td> 100</td>",
" <td> PASS</td>",
" <td> GT:DS:GL</td>",
" </tr>",
" <tr>",
" <th>rs192339082</th>",
" <td> 22</td>",
" <td> 16051477</td>",
" <td> C</td>",
" <td> A</td>",
" <td> 100</td>",
" <td> PASS</td>",
" <td> GT:DS:GL</td>",
" </tr>",
" <tr>",
" <th>rs79725552</th>",
" <td> 22</td>",
" <td> 16051480</td>",
" <td> T</td>",
" <td> C</td>",
" <td> 100</td>",
" <td> PASS</td>",
" <td> GT:DS:GL</td>",
" </tr>",
" </tbody>",
"</table>",
"</div>"
],
"output_type": "pyout",
"prompt_number": 3,
"text": [
" #CHROM POS REF ALT QUAL FILTER FORMAT",
"rs149201999 22 16050408 T C 100 PASS GT:DS:GL",
"rs146752890 22 16050612 C G 100 PASS GT:DS:GL",
"rs139377059 22 16050678 C T 100 PASS GT:DS:GL",
"rs188945759 22 16050984 C G 100 PASS GT:DS:GL",
"rs6518357 22 16051107 C A 100 PASS GT:DS:GL",
"rs62224609 22 16051249 T C 100 PASS GT:DS:GL",
"rs62224610 22 16051347 G C 100 PASS GT:DS:GL",
"rs143503259 22 16051453 A C 100 PASS GT:DS:GL",
"rs192339082 22 16051477 C A 100 PASS GT:DS:GL",
"rs79725552 22 16051480 T C 100 PASS GT:DS:GL"
]
}
],
"prompt_number": 3
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"#Preview genotype matrix",
"v.geno.ix[0:10,0:7]"
],
"language": "python",
"outputs": [
{
"html": [
"<div style=\"max-height:1000px;max-width:1500px;overflow:auto;\">",
"<table border=\"1\" class=\"dataframe\">",
" <thead>",
" <tr style=\"text-align: right;\">",
" <th></th>",
" <th>HG00096</th>",
" <th>HG00097</th>",
" <th>HG00099</th>",
" <th>HG00100</th>",
" <th>HG00101</th>",
" <th>HG00102</th>",
" <th>HG00103</th>",
" </tr>",
" </thead>",
" <tbody>",
" <tr>",
" <th>rs149201999</th>",
" <td> 0</td>",
" <td> 1</td>",
" <td> 1</td>",
" <td> 0</td>",
" <td> 1</td>",
" <td> 1</td>",
" <td> 0</td>",
" </tr>",
" <tr>",
" <th>rs146752890</th>",
" <td> 1</td>",
" <td> 1</td>",
" <td> 1</td>",
" <td> 0</td>",
" <td> 1</td>",
" <td> 0</td>",
" <td> 0</td>",
" </tr>",
" <tr>",
" <th>rs139377059</th>",
" <td> 0</td>",
" <td> 1</td>",
" <td> 1</td>",
" <td> 0</td>",
" <td> 1</td>",
" <td> 1</td>",
" <td> 0</td>",
" </tr>",
" <tr>",
" <th>rs188945759</th>",
" <td> 0</td>",
" <td> 0</td>",
" <td> 0</td>",
" <td> 0</td>",
" <td> 0</td>",
" <td> 0</td>",
" <td> 0</td>",
" </tr>",
" <tr>",
" <th>rs6518357</th>",
" <td> 0</td>",
" <td> 1</td>",
" <td> 1</td>",
" <td> 0</td>",
" <td> 1</td>",
" <td> 1</td>",
" <td> 0</td>",
" </tr>",
" <tr>",
" <th>rs62224609</th>",
" <td> 0</td>",
" <td> 1</td>",
" <td> 1</td>",
" <td> 0</td>",
" <td> 0</td>",
" <td> 1</td>",
" <td> 0</td>",
" </tr>",
" <tr>",
" <th>rs62224610</th>",
" <td> 0</td>",
" <td> 1</td>",
" <td> 1</td>",
" <td> 1</td>",
" <td> 1</td>",
" <td> 1</td>",
" <td> 0</td>",
" </tr>",
" <tr>",
" <th>rs143503259</th>",
" <td> 0</td>",
" <td> 1</td>",
" <td> 1</td>",
" <td> 0</td>",
" <td> 0</td>",
" <td> 1</td>",
" <td> 0</td>",
" </tr>",
" <tr>",
" <th>rs192339082</th>",
" <td> 0</td>",
" <td> 0</td>",
" <td> 0</td>",
" <td> 0</td>",
" <td> 0</td>",
" <td> 0</td>",
" <td> 0</td>",
" </tr>",
" <tr>",
" <th>rs79725552</th>",
" <td> 0</td>",
" <td> 1</td>",
" <td> 1</td>",
" <td> 0</td>",
" <td> 1</td>",
" <td> 1</td>",
" <td> 0</td>",
" </tr>",
" </tbody>",
"</table>",
"</div>"
],
"output_type": "pyout",
"prompt_number": 4,
"text": [
" HG00096 HG00097 HG00099 HG00100 HG00101 HG00102 HG00103",
"rs149201999 0 1 1 0 1 1 0",
"rs146752890 1 1 1 0 1 0 0",
"rs139377059 0 1 1 0 1 1 0",
"rs188945759 0 0 0 0 0 0 0",
"rs6518357 0 1 1 0 1 1 0",
"rs62224609 0 1 1 0 0 1 0",
"rs62224610 0 1 1 1 1 1 0",
"rs143503259 0 1 1 0 0 1 0",
"rs192339082 0 0 0 0 0 0 0",
"rs79725552 0 1 1 0 1 1 0"
]
}
],
"prompt_number": 4
},
{
"cell_type": "code",
"collapsed": true,
"input": [],
"language": "python",
"outputs": [],
"prompt_number": 4
},
{
"cell_type": "code",
"collapsed": true,
"input": [
"#Load in data from a SNP array which is formatted with both alleles in one column (eg. 23 and me data)",
"s = SNP_array('./tests/data/one-column-test-data', fileformat='one column', delim = '\\t',",
" encoding = {'rs4477212':'A/G','rs3094315':'A/G','rs3131972':'G/A','rs12124819':'A/G','rs11240777':'A/G',\\",
" 'rs6681049':'C/T','rs4970383':'T/C','rs4475691':'T/C','rs7537756':'A/T'})"
],
"language": "python",
"outputs": [],
"prompt_number": 5
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"#Preview data from SNP array",
"s.df.ix[0:10,:]"
],
"language": "python",
"outputs": [
{
"html": [
"<div style=\"max-height:1000px;max-width:1500px;overflow:auto;\">",
"<table border=\"1\" class=\"dataframe\">",
" <thead>",
" <tr style=\"text-align: right;\">",
" <th></th>",
" <th>rsid</th>",
" <th>chromosome</th>",
" <th>position</th>",
" <th>genotype</th>",
" </tr>",
" <tr>",
" <th>rsid</th>",
" <th></th>",
" <th></th>",
" <th></th>",
" <th></th>",
" </tr>",
" </thead>",
" <tbody>",
" <tr>",
" <th>rs4477212</th>",
" <td> rs4477212</td>",
" <td> 1</td>",
" <td> 72017</td>",
" <td> AA</td>",
" </tr>",
" <tr>",
" <th>rs3094315</th>",
" <td> rs3094315</td>",
" <td> 1</td>",
" <td> 742429</td>",
" <td> AA</td>",
" </tr>",
" <tr>",
" <th>rs3131972</th>",
" <td> rs3131972</td>",
" <td> 1</td>",
" <td> 742584</td>",
" <td> GG</td>",
" </tr>",
" <tr>",
" <th>rs12124819</th>",
" <td> rs12124819</td>",
" <td> 1</td>",
" <td> 766409</td>",
" <td> AG</td>",
" </tr>",
" <tr>",
" <th>rs11240777</th>",
" <td> rs11240777</td>",
" <td> 1</td>",
" <td> 788822</td>",
" <td> GG</td>",
" </tr>",
" <tr>",
" <th>rs6681049</th>",
" <td> rs6681049</td>",
" <td> 1</td>",
" <td> 789870</td>",
" <td> CC</td>",
" </tr>",
" <tr>",
" <th>rs4970383</th>",
" <td> rs4970383</td>",
" <td> 1</td>",
" <td> 828418</td>",
" <td> CC</td>",
" </tr>",
" <tr>",
" <th>rs4475691</th>",
" <td> rs4475691</td>",
" <td> 1</td>",
" <td> 836671</td>",
" <td> CC</td>",
" </tr>",
" <tr>",
" <th>rs7537756</th>",
" <td> rs7537756</td>",
" <td> 1</td>",
" <td> 844113</td>",
" <td> AA</td>",
" </tr>",
" </tbody>",
"</table>",
"</div>"
],
"output_type": "pyout",
"prompt_number": 6,
"text": [
" rsid chromosome position genotype",
"rsid ",
"rs4477212 rs4477212 1 72017 AA",
"rs3094315 rs3094315 1 742429 AA",
"rs3131972 rs3131972 1 742584 GG",
"rs12124819 rs12124819 1 766409 AG",
"rs11240777 rs11240777 1 788822 GG",
"rs6681049 rs6681049 1 789870 CC",
"rs4970383 rs4970383 1 828418 CC",
"rs4475691 rs4475691 1 836671 CC",
"rs7537756 rs7537756 1 844113 AA"
]
}
],
"prompt_number": 6
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"#Preview genotype data from SNP array",
"s.geno.ix[0:10,:]"
],
"language": "python",
"outputs": [
{
"html": [
"<div style=\"max-height:1000px;max-width:1500px;overflow:auto;\">",
"<table border=\"1\" class=\"dataframe\">",
" <thead>",
" <tr style=\"text-align: right;\">",
" <th></th>",
" <th>genotype</th>",
" </tr>",
" <tr>",
" <th>rsid</th>",
" <th></th>",
" </tr>",
" </thead>",
" <tbody>",
" <tr>",
" <th>rs4477212</th>",
" <td> 0</td>",
" </tr>",
" <tr>",
" <th>rs3094315</th>",
" <td> 0</td>",
" </tr>",
" <tr>",
" <th>rs3131972</th>",
" <td> 0</td>",
" </tr>",
" <tr>",
" <th>rs12124819</th>",
" <td> 1</td>",
" </tr>",
" <tr>",
" <th>rs11240777</th>",
" <td> 2</td>",
" </tr>",
" <tr>",
" <th>rs6681049</th>",
" <td> 0</td>",
" </tr>",
" <tr>",
" <th>rs4970383</th>",
" <td> 2</td>",
" </tr>",
" <tr>",
" <th>rs4475691</th>",
" <td> 2</td>",
" </tr>",
" <tr>",
" <th>rs7537756</th>",
" <td> 0</td>",
" </tr>",
" </tbody>",
"</table>",
"</div>"
],
"output_type": "pyout",
"prompt_number": 7,
"text": [
" genotype",
"rsid ",
"rs4477212 0",
"rs3094315 0",
"rs3131972 0",
"rs12124819 1",
"rs11240777 2",
"rs6681049 0",
"rs4970383 2",
"rs4475691 2",
"rs7537756 0"
]
}
],
"prompt_number": 7
},
{
"cell_type": "code",
"collapsed": true,
"input": [
"#Load in data form a SNP array with two columns representing the alleles of an individual",
"t = SNP_array('tests/data/two-column-test-data', fileformat = 'two column', delim = '\\t',\\",
" encoding = {'rs4477212':'A/G','rs3094315':'A/G','rs3131972':'G/A','rs12124819':'A/G',\\",
" 'rs11240777':'A/G','rs6681049':'C/T','rs4970383':'T/C','rs4475691':'T/C','rs7537756':'A/T'})"
],
"language": "python",
"outputs": [],
"prompt_number": 8
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"#Preview data",
"t.df.ix[0:10,0:4]"
],
"language": "python",
"outputs": [
{
"html": [
"<div style=\"max-height:1000px;max-width:1500px;overflow:auto;\">",
"<table border=\"1\" class=\"dataframe\">",
" <thead>",
" <tr style=\"text-align: right;\">",
" <th></th>",
" <th>chromosome</th>",
" <th>Snp.ID</th>",
" <th>genetic.position</th>",
" <th>bp.position</th>",
" </tr>",
" <tr>",
" <th>Snp.ID</th>",
" <th></th>",
" <th></th>",
" <th></th>",
" <th></th>",
" </tr>",
" </thead>",
" <tbody>",
" <tr>",
" <th>rs4477212</th>",
" <td> 1</td>",
" <td> rs4477212</td>",
" <td> 0</td>",
" <td> 72017</td>",
" </tr>",
" <tr>",
" <th>rs3094315</th>",
" <td> 1</td>",
" <td> rs3094315</td>",
" <td> 0</td>",
" <td> 742429</td>",
" </tr>",
" <tr>",
" <th>rs3131972</th>",
" <td> 1</td>",
" <td> rs3131972</td>",
" <td> 0</td>",
" <td> 742584</td>",
" </tr>",
" <tr>",
" <th>rs12124819</th>",
" <td> 1</td>",
" <td> rs12124819</td>",
" <td> 0</td>",
" <td> 766409</td>",
" </tr>",
" <tr>",
" <th>rs11240777</th>",
" <td> 1</td>",
" <td> rs11240777</td>",
" <td> 0</td>",
" <td> 788822</td>",
" </tr>",
" <tr>",
" <th>rs6681049</th>",
" <td> 1</td>",
" <td> rs6681049</td>",
" <td> 0</td>",
" <td> 789870</td>",
" </tr>",
" <tr>",
" <th>rs4970383</th>",
" <td> 1</td>",
" <td> rs4970383</td>",
" <td> 0</td>",
" <td> 828418</td>",
" </tr>",
" <tr>",
" <th>rs4475691</th>",
" <td> 1</td>",
" <td> rs4475691</td>",
" <td> 0</td>",
" <td> 836671</td>",
" </tr>",
" <tr>",
" <th>rs7537756</th>",
" <td> 1</td>",
" <td> rs7537756</td>",
" <td> 0</td>",
" <td> 844113</td>",
" </tr>",
" </tbody>",
"</table>",
"</div>"
],
"output_type": "pyout",
"prompt_number": 9,
"text": [
" chromosome Snp.ID genetic.position bp.position",
"Snp.ID ",
"rs4477212 1 rs4477212 0 72017",
"rs3094315 1 rs3094315 0 742429",
"rs3131972 1 rs3131972 0 742584",
"rs12124819 1 rs12124819 0 766409",
"rs11240777 1 rs11240777 0 788822",
"rs6681049 1 rs6681049 0 789870",
"rs4970383 1 rs4970383 0 828418",
"rs4475691 1 rs4475691 0 836671",
"rs7537756 1 rs7537756 0 844113"
]
}
],
"prompt_number": 9
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"#Preview genotype matrix",
"t.geno.ix[0:10,0:7]"
],
"language": "python",
"outputs": [
{
"html": [
"<div style=\"max-height:1000px;max-width:1500px;overflow:auto;\">",
"<table border=\"1\" class=\"dataframe\">",
" <thead>",
" <tr style=\"text-align: right;\">",
" <th></th>",
" <th>person1_alle</th>",
" <th>person2_alle</th>",
" </tr>",
" <tr>",
" <th>Snp.ID</th>",
" <th></th>",
" <th></th>",
" </tr>",
" </thead>",
" <tbody>",
" <tr>",
" <th>rs4477212</th>",
" <td> 0</td>",
" <td> 0</td>",
" </tr>",
" <tr>",
" <th>rs3094315</th>",
" <td> 0</td>",
" <td> 1</td>",
" </tr>",
" <tr>",
" <th>rs3131972</th>",
" <td> 0</td>",
" <td> 1</td>",
" </tr>",
" <tr>",
" <th>rs12124819</th>",
" <td> 1</td>",
" <td> 1</td>",
" </tr>",
" <tr>",
" <th>rs11240777</th>",
" <td> 2</td>",
" <td> 2</td>",
" </tr>",
" <tr>",
" <th>rs6681049</th>",
" <td> 0</td>",
" <td> 1</td>",
" </tr>",
" <tr>",
" <th>rs4970383</th>",
" <td> 2</td>",
" <td> 2</td>",
" </tr>",
" <tr>",
" <th>rs4475691</th>",
" <td> 2</td>",
" <td> 0</td>",
" </tr>",
" <tr>",
" <th>rs7537756</th>",
" <td> 0</td>",
" <td> 1</td>",
" </tr>",
" </tbody>",
"</table>",
"</div>"
],
"output_type": "pyout",
"prompt_number": 10,
"text": [
" person1_alle person2_alle",
"Snp.ID ",
"rs4477212 0 0",
"rs3094315 0 1",
"rs3131972 0 1",
"rs12124819 1 1",
"rs11240777 2 2",
"rs6681049 0 1",
"rs4970383 2 2",
"rs4475691 2 0",
"rs7537756 0 1"
]
}
],
"prompt_number": 10
},
{
"cell_type": "code",
"collapsed": true,
"input": [],
"language": "python",
"outputs": [],
"prompt_number": 10
},
{
"cell_type": "code",
"collapsed": true,
"input": [
"#Load in a PED file",
"p = PED('tests/data/test.ped', 'tests/data/test.map', {'snp1':'A/C','snp2':'A/C','snp3':'C/A','snp4':'T/G','snp5':'C/A'})"
],
"language": "python",
"outputs": [],
"prompt_number": 11
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"#See the parsed out PED file",
"p.PED"
],
"language": "python",
"outputs": [
{
"html": [
"<div style=\"max-height:1000px;max-width:1500px;overflow:auto;\">",
"<table border=\"1\" class=\"dataframe\">",
" <thead>",
" <tr style=\"text-align: right;\">",
" <th></th>",
" <th>0</th>",
" <th>1</th>",
" <th>2</th>",
" <th>3</th>",
" <th>4</th>",
" <th>5</th>",
" <th>6</th>",
" <th>7</th>",
" <th>8</th>",
" <th>9</th>",
" <th>10</th>",
" <th>11</th>",
" <th>12</th>",
" <th>13</th>",
" <th>14</th>",
" <th>15</th>",
" </tr>",
" </thead>",
" <tbody>",
" <tr>",
" <th>0</th>",
" <td> 1</td>",
" <td> sample1</td>",
" <td> 0</td>",
" <td> 0</td>",
" <td> 1</td>",
" <td> 1</td>",
" <td> A</td>",
" <td> A</td>",
" <td> A</td>",
" <td> A</td>",
" <td> A</td>",
" <td> A</td>",
" <td> T</td>",
" <td> G</td>",
" <td> A</td>",
" <td> A</td>",
" </tr>",
" <tr>",
" <th>1</th>",
" <td> 2</td>",
" <td> sample2</td>",
" <td> 0</td>",
" <td> 0</td>",
" <td> 1</td>",
" <td> 1</td>",
" <td> A</td>",
" <td> C</td>",
" <td> A</td>",
" <td> C</td>",
" <td> A</td>",
" <td> C</td>",
" <td> T</td>",
" <td> G</td>",
" <td> A</td>",
" <td> C</td>",
" </tr>",
" <tr>",
" <th>2</th>",
" <td> 3</td>",
" <td> sample3</td>",
" <td> 0</td>",
" <td> 0</td>",
" <td> 2</td>",
" <td> 1</td>",
" <td> A</td>",
" <td> A</td>",
" <td> A</td>",
" <td> A</td>",
" <td> A</td>",
" <td> A</td>",
" <td> G</td>",
" <td> G</td>",
" <td> A</td>",
" <td> A</td>",
" </tr>",
" <tr>",
" <th>3</th>",
" <td> 4</td>",
" <td> sample4</td>",
" <td> 0</td>",
" <td> 0</td>",
" <td> 2</td>",
" <td> 1</td>",
" <td> A</td>",
" <td> 0</td>",
" <td> A</td>",
" <td> C</td>",
" <td> A</td>",
" <td> C</td>",
" <td> G</td>",
" <td> G</td>",
" <td> A</td>",
" <td> C</td>",
" </tr>",
" </tbody>",
"</table>",
"</div>"
],
"output_type": "pyout",
"prompt_number": 12,
"text": [
" 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15",
"0 1 sample1 0 0 1 1 A A A A A A T G A A",
"1 2 sample2 0 0 1 1 A C A C A C T G A C",
"2 3 sample3 0 0 2 1 A A A A A A G G A A",
"3 4 sample4 0 0 2 1 A 0 A C A C G G A C"
]
}
],
"prompt_number": 12
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"#See parsed out MAP file",
"p.MAP"
],
"language": "python",
"outputs": [
{
"html": [
"<div style=\"max-height:1000px;max-width:1500px;overflow:auto;\">",
"<table border=\"1\" class=\"dataframe\">",
" <thead>",
" <tr style=\"text-align: right;\">",
" <th></th>",
" <th>0</th>",
" <th>1</th>",
" <th>2</th>",
" <th>3</th>",
" </tr>",
" </thead>",
" <tbody>",
" <tr>",
" <th>0</th>",
" <td> 1</td>",
" <td> snp1</td>",
" <td> 0</td>",
" <td> 1000</td>",
" </tr>",
" <tr>",
" <th>1</th>",
" <td> X</td>",
" <td> snp2</td>",
" <td> 0</td>",
" <td> 1000</td>",
" </tr>",
" <tr>",
" <th>2</th>",
" <td> Y</td>",
" <td> snp3</td>",
" <td> 0</td>",
" <td> 1000</td>",
" </tr>",
" <tr>",
" <th>3</th>",
" <td> XY</td>",
" <td> snp4</td>",
" <td> 0</td>",
" <td> 1000</td>",
" </tr>",
" <tr>",
" <th>4</th>",
" <td> MT</td>",
" <td> snp5</td>",
" <td> 0</td>",
" <td> 1000</td>",
" </tr>",
" </tbody>",
"</table>",
"</div>"
],
"output_type": "pyout",
"prompt_number": 13,
"text": [
" 0 1 2 3",
"0 1 snp1 0 1000",
"1 X snp2 0 1000",
"2 Y snp3 0 1000",
"3 XY snp4 0 1000",
"4 MT snp5 0 1000"
]
}
],
"prompt_number": 13
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"#Vieing the genotype matrix",
"p.geno"
],
"language": "python",
"outputs": [
{
"html": [
"<div style=\"max-height:1000px;max-width:1500px;overflow:auto;\">",
"<table border=\"1\" class=\"dataframe\">",
" <thead>",
" <tr style=\"text-align: right;\">",
" <th>1</th>",
" <th>sample1</th>",
" <th>sample2</th>",
" <th>sample3</th>",
" <th>sample4</th>",
" </tr>",
" <tr>",
" <th>1</th>",
" <th></th>",
" <th></th>",
" <th></th>",
" <th></th>",
" </tr>",
" </thead>",
" <tbody>",
" <tr>",
" <th>snp1</th>",
" <td> 0</td>",
" <td> 1</td>",
" <td> 0</td>",
" <td>NaN</td>",
" </tr>",
" <tr>",
" <th>snp2</th>",
" <td> 0</td>",
" <td> 1</td>",
" <td> 0</td>",
" <td> 1</td>",
" </tr>",
" <tr>",
" <th>snp3</th>",
" <td> 2</td>",
" <td> 1</td>",
" <td> 2</td>",
" <td> 1</td>",
" </tr>",
" <tr>",
" <th>snp4</th>",
" <td> 1</td>",
" <td> 1</td>",
" <td> 2</td>",
" <td> 2</td>",
" </tr>",
" <tr>",
" <th>snp5</th>",
" <td> 2</td>",
" <td> 1</td>",
" <td> 2</td>",
" <td> 1</td>",
" </tr>",
" </tbody>",
"</table>",
"</div>"
],
"output_type": "pyout",
"prompt_number": 14,
"text": [
"1 sample1 sample2 sample3 sample4",
"1 ",
"snp1 0 1 0 NaN",
"snp2 0 1 0 1",
"snp3 2 1 2 1",
"snp4 1 1 2 2",
"snp5 2 1 2 1"
]
}
],
"prompt_number": 14
}
]
}
]
}
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