initialise

c9b0ed92 · Rauschenberger · c9b0ed92 · c9b0ed92 · c9b0ed92 · c9b0ed92
Commit c9b0ed92 authored Jun 14, 2018 by Rauschenberger
38 changed files
--- a/.Rbuildignore
+++ b/.Rbuildignore
+^Readme\.Rmd$
+^\.travis\.yml$
+^_pkgdown\.yml$
+^docs$
+^cran-comments\.md$
+^appveyor\.yml$
--- a/.travis.yml
+++ b/.travis.yml
+# R for travis: see documentation at https://docs.travis-ci.com/user/languages/r
+
+language: R
+
+
+os:
+  - linux
+
+sudo: false	
+cache: packages
+use_bioc: true
+bioc_required: true
+
+r:
+  - devel
+
+r_packages:
+  - covr
+
+after_success:
+  - Rscript -e 'library(covr); codecov()'
--- a/DESCRIPTION
+++ b/DESCRIPTION
+Package: spliceQTL
+Version: 0.0.0
+Title: Alternative Splicing
+Description: Implements test for alternative splicing.
+Depends: R (>= 3.0.0)
+Imports: lme4, globaltest, edgeR, snpStats, refGenome, R.utils, methods
+Suggests: knitr, testthat
+Authors@R: c(person("Armin","Rauschenberger",email="a.rauschenberger@vumc.nl",role=c("aut","cre")),
+             person("Renee","Menezes",role=c("aut")))
+VignetteBuilder: knitr
+License: GPL-3
+LazyData: true
+RoxygenNote: 6.0.1
+URL: https://github.com/rauschenberger/spliceQTL
+BugReports: https://github.com/rauschenberger/spliceQTL/issues
--- a/NAMESPACE
+++ b/NAMESPACE
+# Generated by roxygen2: do not edit by hand
+
+export(adjust.exon.length)
+export(adjust.library.sizes)
+export(drop.trivial.genes)
+export(map.exons)
+export(map.genes)
+export(map.snps)
+export(prepare.data.matrices)
+export(spliceQTL)
--- a/NEWS.md
+++ b/NEWS.md
+## spliceQTL 0.0.0 (2018-06-12)
+
+* Added functions
\ No newline at end of file
--- a/R/function.R
+++ b/R/function.R
--- a/README.Rmd
+++ b/README.Rmd
+
+---
+output: github_document
+---
+
+<!-- Modify xxx.Rmd, not xxx.md! -->
+
+```{r, echo = FALSE}
+knitr::opts_chunk$set(
+  collapse = TRUE,
+  comment = "#>",
+  fig.path = "README-"
+)
+```
+
+## Scope
+
+spliceQTL
+
+## Installation
+
+```{r,eval=FALSE}
+#install.packages("devtools")
+devtools::install_github("rauschenberger/spliceQTL")
+```
+
+## Reference
+
+
--- a/README.md
+++ b/README.md
+
+<!-- Modify xxx.Rmd, not xxx.md! -->
+
+## Scope
+
+spliceQTL
+
+## Installation
+
+``` r
+#install.packages("devtools")
+devtools::install_github("rauschenberger/spliceQTL")
+```
+
+## Reference
--- a/appveyor.yml
+++ b/appveyor.yml
+# DO NOT CHANGE the "init" and "install" sections below
+
+# Download script file from GitHub
+init:
+  ps: |
+        $ErrorActionPreference = "Stop"
+        Invoke-WebRequest http://raw.github.com/krlmlr/r-appveyor/master/scripts/appveyor-tool.ps1 -OutFile "..\appveyor-tool.ps1"
+        Import-Module '..\appveyor-tool.ps1'
+
+install:
+  ps: Bootstrap
+
+cache:
+  - C:\RLibrary
+
+# Adapt as necessary starting from here
+
+build_script:
+  - travis-tool.sh install_bioc_deps
+  - travis-tool.sh install_deps
+
+test_script:
+  - travis-tool.sh run_tests
+
+on_failure:
+  - 7z a failure.zip *.Rcheck\*
+  - appveyor PushArtifact failure.zip
+
+artifacts:
+  - path: '*.Rcheck\**\*.log'
+    name: Logs
+
+  - path: '*.Rcheck\**\*.out'
+    name: Logs
+
+  - path: '*.Rcheck\**\*.fail'
+    name: Logs
+
+  - path: '*.Rcheck\**\*.Rout'
+    name: Logs
+
+  - path: '\*_*.tar.gz'
+    name: Bits
+
+  - path: '\*_*.zip'
+    name: Bits
--- a/docs/articles/index.html
+++ b/docs/articles/index.html
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
+<html>
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+<!-- 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>
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+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]-->
+
+
+  </head>
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+  <body>
+    <div class="container template-article-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>
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+        <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>
+<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>
+      <a href="../articles/vignette.html">spliceQTL</a>
+    </li>
+  </ul>
+</li>
+<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>
+     
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+</li>
+      </ul>
+      
+    </div><!--/.nav-collapse -->
+  </div><!--/.container -->
+</div><!--/.navbar -->
+
+      
+      </header>
+
+<div class="row">
+  <div class="col-md-9 contents">
+    <div class="page-header">
+      <h1>Articles</h1>
+    </div>
+
+    <div class="section ">
+      <h3>All vignettes</h3>
+      <p class="section-desc"></p>
+
+      <ul>
+        <li><a href="vignette.html">spliceQTL</a></li>
+      </ul>
+    </div>
+  </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>
+
+  
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+
--- a/docs/articles/vignette.html
+++ b/docs/articles/vignette.html
+<!DOCTYPE html>
+<!-- Generated by pkgdown: do not edit by hand --><html>
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
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+<!-- 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="spliceQTL">
+<meta property="og:description" content="">
+<meta name="twitter:card" content="summary">
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+<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-article">
+      <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>
+<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>
+      <a href="../articles/vignette.html">spliceQTL</a>
+    </li>
+  </ul>
+</li>
+<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 toc-ignore">
+      <h1>spliceQTL</h1>
+            
+      
+      <small class="dont-index">Source: <a href="https://github.com/rauschenberger/spliceQTL/blob/master/vignettes/vignette.Rmd"><code>vignettes/vignette.Rmd</code></a></small>
+      <div class="hidden name"><code>vignette.Rmd</code></div>
+
+    </div>
+
+    
+    
+<p>rnorm(10)</p>
+  </div>
+
+  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+      </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>
--- a/docs/authors.html
+++ b/docs/authors.html
+<!-- 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">
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+<title>Authors • 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 -->
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+<script src="jquery.sticky-kit.min.js"></script>
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+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]-->
+
+
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+  <body>
+    <div class="container template-authors">
+      <header>
+      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+  <div class="container">
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+        <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">
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+<li>
+  <a href="reference/index.html">Reference</a>
+</li>
+<li class="dropdown">
+  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+    Articles
+     
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+  </a>
+  <ul class="dropdown-menu" role="menu">
+    <li>
+      <a href="articles/vignette.html">spliceQTL</a>
+    </li>
+  </ul>
+</li>
+<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>
+     
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+</li>
+      </ul>
+      
+    </div><!--/.nav-collapse -->
+  </div><!--/.container -->
+</div><!--/.navbar -->
+
+      
+      </header>
+
+<div class="row">
+  <div class="contents col-md-9">
+    <div class="page-header">
+      <h1>Authors</h1>
+    </div>
+
+    <ul class="list-unstyled">
+      <li>
+        <p><strong>Armin Rauschenberger</strong>. Author, maintainer. 
+        </p>
+      </li>
+      <li>
+        <p><strong>Renee Menezes</strong>. Author. 
+        </p>
+      </li>
+    </ul>
+
+  </div>
+
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+
+
+      <footer>
+      <div class="copyright">
+  <p>Developed by Armin Rauschenberger, Renee Menezes.</p>
+</div>
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+</div>
+
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+</html>
+
--- a/docs/docsearch.css
+++ b/docs/docsearch.css
+/* Docsearch -------------------------------------------------------------- */
+/*
+  Source: https://github.com/algolia/docsearch/
+  License: MIT
+*/
+
+.algolia-autocomplete {
+  display: block;
+  -webkit-box-flex: 1;
+  -ms-flex: 1;
+  flex: 1
+}
+
+.algolia-autocomplete .ds-dropdown-menu {
+  width: 100%;
+  min-width: none;
+  max-width: none;
+  padding: .75rem 0;
+  background-color: #fff;
+  background-clip: padding-box;
+  border: 1px solid rgba(0, 0, 0, .1);
+  box-shadow: 0 .5rem 1rem rgba(0, 0, 0, .175);
+}
+
+@media (min-width:768px) {
+  .algolia-autocomplete .ds-dropdown-menu {
+      width: 175%
+  }
+}
+
+.algolia-autocomplete .ds-dropdown-menu::before {
+  display: none
+}
+
+.algolia-autocomplete .ds-dropdown-menu [class^=ds-dataset-] {
+  padding: 0;
+  background-color: rgb(255,255,255);
+  border: 0;
+  max-height: 80vh;
+}
+
+.algolia-autocomplete .ds-dropdown-menu .ds-suggestions {
+  margin-top: 0
+}
+
+.algolia-autocomplete .algolia-docsearch-suggestion {
+  padding: 0;
+  overflow: visible
+}
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+  margin-top: 0;
+  font-size: 1.3em;
+  font-weight: 500;
+  color: #00008B;
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+
+.algolia-autocomplete .algolia-docsearch-suggestion--wrapper {
+    float: none;
+    padding-top: 0
+}
+
+.algolia-autocomplete .algolia-docsearch-suggestion--subcategory-column {
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+.algolia-autocomplete .ds-suggestion .algolia-docsearch-suggestion--subcategory-column {
+  display: block;
+  padding: .1rem 1rem;
+  margin-bottom: 0.1;
+  font-size: 1.0em;
+  font-weight: 400
+  /* display: none */
+}