index.html 7.41 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
<!-- 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>Function reference • 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="Function reference" />


<!-- 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-index">
      <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
73
74
75
76
77
78
79
80
<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
81
      <a href="../articles/code.html">rainbow (code)</a>
Rauschenberger's avatar
Rauschenberger committed
82
    </li>
Rauschenberger's avatar
Rauschenberger committed
83
84
85
    <li>
      <a href="../articles/text.html">rainbow (text)</a>
    </li>
Rauschenberger's avatar
Rauschenberger committed
86
87
  </ul>
</li>
Rauschenberger's avatar
Rauschenberger committed
88
89
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
139
140
141
142
143
144
145
146
147
148
149
<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="contents col-md-9">
    <div class="page-header">
      <h1>Reference</h1>
    </div>

    <table class="ref-index">

    <colgroup>
      <col class="alias" />
      <col class="title" />
    </colgroup>

    <tbody>
      <tr>
        <th colspan="2">
          <h2 id="section-all-functions" class="hasAnchor"><a href="#section-all-functions" class="anchor"></a>All functions</h2>
          <p class="section-desc"></p>
        </th>
      </tr>
      <tr>
        <!--  -->
        <td>
          <p><code><a href="map.genes.html">map.genes()</a></code> </p>
        </td>
        <td><p>Search for genes</p></td>
      </tr><tr>
        <!--  -->
        <td>
          <p><code><a href="map.exons.html">map.exons()</a></code> </p>
        </td>
        <td><p>Search for exons</p></td>
      </tr><tr>
        <!--  -->
        <td>
          <p><code><a href="map.snps.html">map.snps()</a></code> </p>
        </td>
        <td><p>Search for SNPs</p></td>
      </tr><tr>
        <!--  -->
        <td>
Rauschenberger's avatar
Rauschenberger committed
150
          <p><code><a href="match.samples.html">match.samples()</a></code> </p>
Rauschenberger's avatar
Rauschenberger committed
151
152
        </td>
        <td><p>Prepare data matrices</p></td>
Rauschenberger's avatar
Rauschenberger committed
153
154
155
156
157
158
      </tr><tr>
        <!--  -->
        <td>
          <p><code><a href="adjust.samples.html">adjust.samples()</a></code> </p>
        </td>
        <td><p>Adjust library sizes</p></td>
Rauschenberger's avatar
Rauschenberger committed
159
160
161
162
163
      </tr><tr>
        <!--  -->
        <td>
          <p><code><a href="test.single.html">test.single()</a></code> </p>
        </td>
Rauschenberger's avatar
Rauschenberger committed
164
        <td><p>Conduct single test</p></td>
Rauschenberger's avatar
Rauschenberger committed
165
166
167
168
169
170
      </tr><tr>
        <!--  -->
        <td>
          <p><code><a href="test.multiple.html">test.multiple()</a></code> </p>
        </td>
        <td><p>Conduct multiple tests</p></td>
Rauschenberger's avatar
Rauschenberger committed
171
172
173
174
175
      </tr><tr>
        <!--  -->
        <td>
          <p><code><a href="drop.trivial.html">drop.trivial()</a></code> </p>
        </td>
Rauschenberger's avatar
Rauschenberger committed
176
        <td><p>Drop trivial tests</p></td>
Rauschenberger's avatar
Rauschenberger committed
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
      </tr><tr>
        <!--  -->
        <td>
          <p><code><a href="get.snps.geuvadis.html">get.snps.geuvadis()</a></code> </p>
        </td>
        <td><p>Get SNP data (Geuvadis)</p></td>
      </tr><tr>
        <!--  -->
        <td>
          <p><code><a href="get.snps.bbmri.html">get.snps.bbmri()</a></code> </p>
        </td>
        <td><p>Get SNP data (BBMRI)</p></td>
      </tr><tr>
        <!--  -->
        <td>
          <p><code><a href="get.exons.geuvadis.html">get.exons.geuvadis()</a></code> </p>
        </td>
        <td><p>Get exon data (Geuvadis)</p></td>
      </tr><tr>
        <!--  -->
        <td>
          <p><code><a href="get.exons.bbmri.html">get.exons.bbmri()</a></code> </p>
        </td>
        <td><p>Get exon data (BBMRI)</p></td>
Rauschenberger's avatar
Rauschenberger committed
201
202
203
204
205
206
      </tr><tr>
        <!--  -->
        <td>
          <p><code><a href="spliceQTL-package.html">spliceQTL-package</a></code> </p>
        </td>
        <td><p>Alternative Splicing</p></td>
Rauschenberger's avatar
Rauschenberger committed
207
208
209
210
211
212
      </tr><tr>
        <!--  -->
        <td>
          <p><code><a href="adjust.variables.html">adjust.variables()</a></code> </p>
        </td>
        <td><p>Adjust exon length</p></td>
Rauschenberger's avatar
Rauschenberger committed
213
214
215
216
217
218
      </tr><tr>
        <!--  -->
        <td>
          <p><code><a href="grid.html">grid()</a></code> </p>
        </td>
        <td><p>Plot grid</p></td>
Rauschenberger's avatar
Rauschenberger committed
219
220
221
222
223
224
      </tr><tr>
        <!--  -->
        <td>
          <p><code><a href="visualise.html">visualise()</a></code> </p>
        </td>
        <td><p>Plot SNP-exon correlations</p></td>
Rauschenberger's avatar
Rauschenberger committed
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
      </tr>
    </tbody>
    </table>
  </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="#section-all-functions">All functions</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>