spliceQTL-package.html 6.24 KB
Newer Older
Rauschenberger's avatar
Rauschenberger committed
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
<html>
  <head>
  <meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">

<title>Alternative Splicing — spliceQTL-package • spliceQTL</title>

<!-- jquery -->
<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
<!-- Bootstrap -->

<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>

<!-- Font Awesome icons -->
<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">

<!-- clipboard.js -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>

<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
<script src="../jquery.sticky-kit.min.js"></script>
<script src="../pkgdown.js"></script>



<meta property="og:title" content="Alternative Splicing — spliceQTL-package" />

<meta property="og:description" content="This R package includes various functions
for applying the global test of alternative splicing.
Some functions only work on the virtual machine (see below)." />
<meta name="twitter:card" content="summary" />


<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>

<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
<![endif]-->


  </head>

  <body>
    <div class="container template-reference-topic">
      <header>
      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
  <div class="container">
    <div class="navbar-header">
      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
        <span class="icon-bar"></span>
        <span class="icon-bar"></span>
        <span class="icon-bar"></span>
      </button>
      <span class="navbar-brand">
        <a class="navbar-link" href="../index.html">spliceQTL</a>
        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.0.0</span>
      </span>
    </div>

    <div id="navbar" class="navbar-collapse collapse">
      <ul class="nav navbar-nav">
        <li>
  <a href="../index.html">
    <span class="fa fa-home fa-lg"></span>
     
  </a>
</li>
<li>
  <a href="../reference/index.html">Reference</a>
</li>
Rauschenberger's avatar
Rauschenberger committed
78
79
80
81
82
83
84
85
<li class="dropdown">
  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
    Articles
     
    <span class="caret"></span>
  </a>
  <ul class="dropdown-menu" role="menu">
    <li>
Rauschenberger's avatar
Rauschenberger committed
86
      <a href="../articles/code.html">rainbow (code)</a>
Rauschenberger's avatar
Rauschenberger committed
87
88
89
    </li>
  </ul>
</li>
Rauschenberger's avatar
Rauschenberger committed
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
<li>
  <a href="../news/index.html">Changelog</a>
</li>
      </ul>
      
      <ul class="nav navbar-nav navbar-right">
        <li>
  <a href="https://github.com/rauschenberger/spliceQTL">
    <span class="fa fa-github fa-lg"></span>
     
  </a>
</li>
      </ul>
      
    </div><!--/.nav-collapse -->
  </div><!--/.container -->
</div><!--/.navbar -->

      
      </header>

<div class="row">
  <div class="col-md-9 contents">
    <div class="page-header">
    <h1>Alternative Splicing</h1>
    <small class="dont-index">Source: <a href='https://github.com/rauschenberger/spliceQTL/blob/master/R/functions.R'><code>R/functions.R</code></a></small>
    <div class="hidden name"><code>spliceQTL-package.Rd</code></div>
    </div>

    <div class="ref-description">
    
    <p>This R package includes various functions
for applying the global test of alternative splicing.
Some functions only work on the virtual machine (see below).</p>
    
    </div>

        
    <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>

    <div class='dont-index'><p>Prepare BBMRI and Geuvadis data:</p><ul>
<li><p><code><a href='get.snps.geuvadis.html'>get.snps.geuvadis</a></code> (not VM)</p></li>
<li><p><code><a href='get.snps.bbmri.html'>get.snps.bbmri</a></code> (only VM)</p></li>
<li><p><code><a href='get.exons.geuvadis.html'>get.exons.geuvadis</a></code> (only VM)</p></li>
<li><p><code><a href='get.exons.bbmri.html'>get.exons.bbmri</a></code> (only VM)</p></li>
</ul></div>
    <div class='dont-index'><p>Process samples and covariates:</p><ul>
<li><p><code><a href='match.samples.html'>match.samples</a></code></p></li>
<li><p><code><a href='adjust.samples.html'>adjust.samples</a></code></p></li>
Rauschenberger's avatar
Rauschenberger committed
139
<li><p><code><a href='adjust.variables.html'>adjust.variables</a></code></p></li>
Rauschenberger's avatar
Rauschenberger committed
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
</ul></div>
    <div class='dont-index'><p>Search for exons and SNPs:</p><ul>
<li><p><code><a href='map.genes.html'>map.genes</a></code></p></li>
<li><p><code><a href='map.exons.html'>map.exons</a></code></p></li>
<li><p><code><a href='map.snps.html'>map.snps</a></code></p></li>
<li><p><code><a href='drop.trivial.html'>drop.trivial</a></code></p></li>
</ul></div>
    <div class='dont-index'><p>Test for alternative splicing:</p><ul>
<li><p><code><a href='test.single.html'>test.single</a></code></p></li>
<li><p><code><a href='test.multiple.html'>test.multiple</a></code></p></li>
</ul></div>
    

  </div>
  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
    <h2>Contents</h2>
    <ul class="nav nav-pills nav-stacked">
      
      <li><a href="#see-also">See also</a></li>
          </ul>

  </div>
</div>

      <footer>
      <div class="copyright">
  <p>Developed by Armin Rauschenberger, Renee Menezes.</p>
</div>

<div class="pkgdown">
  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
</div>

      </footer>
   </div>

  

  </body>
</html>