Commit 3625726d authored by Rauschenberger's avatar Rauschenberger
Browse files

automation

parent 557394d2
......@@ -176,9 +176,6 @@ adjust.covariates <- function(x,offset,group){
#' @param build
#' integer 49-91
#'
#' @details
#' This functions ...
#'
#' @examples
#' NA
#'
......@@ -221,11 +218,11 @@ map.genes <- function(chr,path=getwd(),release="GRCh37",build=71){
#' @description
#' This function
#'
#' @param gene_id
#' @param gene
#' gene names\strong{:} vector with one entry per gene,
#' including the gene names
#'
#' @param exon_id
#' @param exon
#' exon names\strong{:} vector with one entry per exon,
#' including the corresponding \emph{gene} names
#' (separated by comma if multiple gene names)
......@@ -283,14 +280,11 @@ map.exons <- function(gene,exon){
#' number of base pairs before start position\strong{:}
#' integer
#'
#' @details
#' This function ...
#'
#' @examples
#' gene.chr <- rep(1,times=5)
#' gene.start <- 1:5
#' gene.end <- 2:6
#'
#'
#' snp.chr <- rep(1,times=100)
#' snp.pos <- seq(from=1,to=4.9,length.out=100)
#'
......@@ -381,7 +375,7 @@ drop.trivial.genes <- function(map){
#' @export
#' @title
#' Conduct tests
#' Conduct single tests
#'
#' @description
#' This function
......@@ -409,7 +403,9 @@ drop.trivial.genes <- function(map){
#' size of permutation chunks\strong{:}
#' integer vector
#'
#' @param
#' @param rho
#' correlation\strong{:}
#' numeric vector with values between \eqn{0} and \eqn{1}
#'
#' @details
#' The maximum number of permutations equals \code{sum(steps)}. Permutations is
......@@ -463,10 +459,10 @@ test.single <- function(Y,X,map,i,limit=NULL,steps=NULL,rho=c(0,0.5,1)){
#' @export
#' @title
#' Conduct tests
#' Conduct multiple tests
#'
#' @description
#' This function
#' This function ...
#'
#' @param Y
#' exon expression\strong{:}
......@@ -476,6 +472,10 @@ test.single <- function(Y,X,map,i,limit=NULL,steps=NULL,rho=c(0,0.5,1)){
#' SNP genotype\strong{:}
#' matrix with \eqn{n} rows (samples) and \eqn{q} columns (SNPs)
#'
#' @param map
#' list with names "genes", "exons", and "snps"
#' (output from \code{map.genes}, \code{map.exons}, and \code{map.snps})
#'
#' @param rho
#' correlation\strong{:}
#' numeric vector with values between \eqn{0} and \eqn{1}
......@@ -533,9 +533,6 @@ test.multiple <- function(Y,X,map,rho=c(0,0.5,1)){
#--- spliceQTL test functions --------------------------------------------------
# Function: G2.multin
......@@ -651,8 +648,7 @@ G2.multin <- function(dep.data,indep.data,stand=TRUE,nperm=100,grouping=F,rho=0,
# tau.mat = X' W.rho X, a n*n matrix : both square, symmetric matrices with an equal number of rows
# Output: test statistic (single value)
#
get.g2stat.multin <- function(U, mu, rho, tau.mat)
{
get.g2stat.multin <- function(U, mu, rho, tau.mat){
g2tstat <- NULL
for(xk in 1:length(rho))
{
......
......@@ -89,7 +89,9 @@
<p>rnorm(10)</p>
<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb1-1" data-line-number="1">stats<span class="op">::</span><span class="kw"><a href="http://www.rdocumentation.org/packages/stats/topics/Normal">rnorm</a></span>(<span class="dv">10</span>)</a></code></pre></div>
<pre><code>## [1] -0.5102516 -0.9053667 -0.3843858 -0.2003901 -0.8825564 -0.4837392
## [7] -0.2320180 0.9918950 1.0735842 0.2360493</code></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
......
......@@ -131,19 +131,14 @@
</tr>
<tr>
<th>offset</th>
<td><p>exon start positions<strong>:</strong> vector of length \(p\)
exon end positions<strong>:</strong> vector of length \(p\)</p></td>
<td><p>exon length<strong>:</strong> vector of length \(p\)</p></td>
</tr>
<tr>
<th>group</th>
<td><p>gene (not exon) names<strong>:</strong> vector of length \(p\)</p></td>
<td><p>gene names<strong>:</strong> vector of length \(p\)</p></td>
</tr>
</table>
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>No information on chromosomes required.</p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><div class='input'><span class='fl'>NA</span></div><div class='output co'>#&gt; [1] NA</div><div class='input'>
......@@ -153,9 +148,7 @@ exon end positions<strong>:</strong> vector of length \(p\)</p></td>
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
<li><a href="#details">Details</a></li>
<li><a href="#examples">Examples</a></li>
</ul>
......
......@@ -133,7 +133,21 @@
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><div class='input'><span class='fl'>NA</span></div><div class='output co'>#&gt; [1] NA</div><div class='input'>
<pre class="examples"><div class='input'><span class='no'>n</span> <span class='kw'>&lt;-</span> <span class='fl'>5</span>; <span class='no'>p</span> <span class='kw'>&lt;-</span> <span class='fl'>10</span>
<span class='no'>x</span> <span class='kw'>&lt;-</span> <span class='fu'>matrix</span>(<span class='fu'>rnbinom</span>(<span class='kw'>n</span><span class='kw'>=</span><span class='no'>n</span>*<span class='no'>p</span>,<span class='kw'>mu</span><span class='kw'>=</span><span class='fl'>5</span>,<span class='kw'>size</span><span class='kw'>=</span><span class='fl'>1</span>/<span class='fl'>0.5</span>),<span class='kw'>nrow</span><span class='kw'>=</span><span class='no'>n</span>,<span class='kw'>ncol</span><span class='kw'>=</span><span class='no'>p</span>)
<span class='no'>x</span>[<span class='fl'>1</span>,] <span class='kw'>&lt;-</span> <span class='fl'>10</span>*<span class='no'>x</span>[<span class='fl'>1</span>,]
<span class='fu'>adjust.samples</span>(<span class='no'>x</span>)</div><div class='output co'>#&gt; [,1] [,2] [,3] [,4] [,5] [,6] [,7]
#&gt; [1,] 26.34421 5.854269 8.781404 38.052751 20.489943 20.48994 67.324097
#&gt; [2,] 35.07730 5.011043 15.033129 10.022086 5.011043 10.02209 50.110429
#&gt; [3,] 11.06749 38.736227 44.269974 0.000000 44.269974 16.60124 5.533747
#&gt; [4,] 48.24565 18.556021 11.133613 11.133613 11.133613 18.55602 7.422408
#&gt; [5,] 44.43728 12.119257 8.079505 8.079505 24.238514 0.00000 48.477028
#&gt; [,8] [,9] [,10]
#&gt; [1,] 32.19848 23.417077 40.97989
#&gt; [2,] 60.13251 35.077300 0.00000
#&gt; [3,] 11.06749 22.134987 77.47245
#&gt; [4,] 44.53445 3.711204 51.95686
#&gt; [5,] 16.15901 16.159009 0.00000</div><div class='input'>
</div></pre>
</div>
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......
......@@ -170,7 +170,13 @@
<td>
<p><code><a href="test.single.html">test.single()</a></code> </p>
</td>
<td><p>Conduct tests</p></td>
<td><p>Conduct single tests</p></td>
</tr><tr>
<!-- -->
<td>
<p><code><a href="test.multiple.html">test.multiple()</a></code> </p>
</td>
<td><p>Conduct multiple tests</p></td>
</tr>
</tbody>
</table>
......
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<h1>Search for exons</h1>
<small class="dont-index">Source: <a href='https://github.com/rauschenberger/spliceQTL/blob/master/R/function.R'><code>R/function.R</code></a></small>
<div class="hidden name"><code>map.exons.Rd</code></div>
</div>
<div class="ref-description">
<p>This function</p>
</div>
<pre class="usage"><span class='fu'>map.exons</span>(<span class='no'>gene_id</span>, <span class='no'>exon_id</span>)</pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
<th>gene_id</th>
<td><p>gene names<strong>:</strong> vector with one entry per gene (gene names!)</p></td>
</tr>
<tr>
<th>exon_id</th>
<td><p>exon names<strong>:</strong> vector with one entry per exon
(also gene names! separated by comma if multiple genes)</p></td>
</tr>
</table>
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>The exon names should contain the gene names. For each gene, this function
returns the indices of the exons.</p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><div class='input'><span class='fl'>NA</span></div><div class='output co'>#&gt; [1] NA</div><div class='input'>
</div></pre>
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<h2>Contents</h2>
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<li><a href="#arguments">Arguments</a></li>
<li><a href="#details">Details</a></li>
<li><a href="#examples">Examples</a></li>
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<h1>Search for exons</h1>
<small class="dont-index">Source: <a href='https://github.com/rauschenberger/spliceQTL/blob/master/R/function.R'><code>R/function.R</code></a></small>
<div class="hidden name"><code>map.exons.Rd</code></div>
</div>
<div class="ref-description">
<p>This function</p>
</div>
<pre class="usage"><span class='fu'>map.exons</span>(<span class='no'>gene</span>, <span class='no'>exon</span>)</pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
<th>gene</th>
<td><p>gene names<strong>:</strong> vector with one entry per gene,
including the gene names</p></td>
</tr>
<tr>
<th>exon</th>
<td><p>exon names<strong>:</strong> vector with one entry per exon,
including the corresponding <em>gene</em> names
(separated by comma if multiple gene names)</p></td>
</tr>
</table>
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>The exon names should contain the gene names. For each gene, this function
returns the indices of the exons.</p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><div class='input'><span class='no'>gene</span> <span class='kw'>&lt;-</span> <span class='fu'>c</span>(<span class='st'>"A"</span>,<span class='st'>"B"</span>,<span class='st'>"C"</span>)
<span class='no'>exon</span> <span class='kw'>&lt;-</span> <span class='fu'>c</span>(<span class='st'>"A"</span>,<span class='st'>"A,B"</span>,<span class='st'>"B"</span>,<span class='st'>"B,C"</span>,<span class='st'>"C"</span>)
<span class='fu'>map.exons</span>(<span class='no'>gene</span>,<span class='no'>exon</span>)</div><div class='output co'>#&gt; | | | 0% | |======================= | 33% | |=============================================== | 67% | |======================================================================| 100%</div><div class='output co'>#&gt; $A
#&gt; [1] 1 2
#&gt;
#&gt; $B
#&gt; [1] 2 3 4
#&gt;
#&gt; $C
#&gt; [1] 4 5
#&gt; </div><div class='input'>
</div></pre>
</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="#arguments">Arguments</a></li>
<li><a href="#details">Details</a></li>
<li><a href="#examples">Examples</a></li>
</ul>
</div>
</div>
<footer>
<div class="copyright">
<p>Developed by Armin Rauschenberger, Renee Menezes.</p>
</div>
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......
......@@ -120,7 +120,7 @@
</div>
<pre class="usage"><span class='fu'>map.genes</span>(<span class='no'>chr</span>, <span class='kw'>path</span> <span class='kw'>=</span> <span class='fu'>getwd</span>(), <span class='kw'>release</span> <span class='kw'>=</span> <span class='st'>"GRCh37"</span>, <span class='kw'>build</span> <span class='kw'>=</span> <span class='st'>"71"</span>)</pre>
<pre class="usage"><span class='fu'>map.genes</span>(<span class='no'>chr</span>, <span class='kw'>path</span> <span class='kw'>=</span> <span class='fu'>getwd</span>(), <span class='kw'>release</span> <span class='kw'>=</span> <span class='st'>"GRCh37"</span>, <span class='kw'>build</span> <span class='kw'>=</span> <span class='fl'>71</span>)</pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
......@@ -143,10 +143,6 @@
</tr>
</table>
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>This functions ...</p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><div class='input'><span class='fl'>NA</span></div><div class='output co'>#&gt; [1] NA</div><div class='input'>
......@@ -156,9 +152,7 @@
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
<li><a href="#details">Details</a></li>
<li><a href="#examples">Examples</a></li>
</ul>
......
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