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Commit ea683705 authored by Rauschenberger's avatar Rauschenberger
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parent d05acde4
# Generated by roxygen2: do not edit by hand
export(adjust.covariates)
export(adjust.samples)
export(adjust.variables)
export(drop.trivial)
export(get.exons.bbmri)
export(get.exons.geuvadis)
......
......@@ -483,7 +483,7 @@ adjust.samples <- function(x){
#' @examples
#' NA
#'
adjust.covariates <- function(x,offset,group){
adjust.variables <- function(x,offset,group){
if(!is.numeric(x)|!is.matrix(x)){
stop("Argument \"x\" is no numeric matrix.",call.=FALSE)
}
......
......@@ -5,11 +5,11 @@
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......@@ -52,10 +52,7 @@
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......@@ -82,7 +79,7 @@
</header><div class="row">
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<h1>code</h1>
<h1>rainbow (code)</h1>
<small class="dont-index">Source: <a href="https://github.com/rauschenberger/spliceQTL/blob/master/vignettes/code.Rmd"><code>vignettes/code.Rmd</code></a></small>
......@@ -110,7 +107,7 @@
<a class="sourceLine" id="cb3-3" data-line-number="3">}</a>
<a class="sourceLine" id="cb3-4" data-line-number="4">spliceQTL<span class="op">::</span><span class="kw"><a href="http://www.rdocumentation.org/packages/spliceQTL/topics/get.exons.geuvadis">get.exons.geuvadis</a></span>(<span class="dt">path=</span>path)</a>
<a class="sourceLine" id="cb3-5" data-line-number="5">spliceQTL<span class="op">::</span><span class="kw"><a href="http://www.rdocumentation.org/packages/spliceQTL/topics/get.exons.bbmri">get.exons.bbmri</a></span>(<span class="dt">path=</span>path)</a></code></pre></div>
<p>On the virtual machine, execute this chunk to prepare the data. See the documentation of the R package spliceQTL for further information. (It seems that lme4::lmer in spliceQTL::adjust.covariates fails to release memory. Restart R after each chromosome.)</p>
<p>On the virtual machine, execute this chunk to prepare the data. See the documentation of the R package spliceQTL for further information. (It seems that lme4::lmer in spliceQTL::adjust.variables fails to release memory. Restart R after each chromosome.)</p>
<div class="sourceCode" id="cb4"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb4-1" data-line-number="1"><span class="cf">for</span>(chr <span class="cf">in</span> <span class="dv">1</span><span class="op">:</span><span class="dv">22</span>){</a>
<a class="sourceLine" id="cb4-2" data-line-number="2"> <span class="cf">for</span>(data <span class="cf">in</span> <span class="kw">c</span>(<span class="st">"Geuvadis"</span>,<span class="st">"LLS"</span>)){</a>
<a class="sourceLine" id="cb4-3" data-line-number="3"> </a>
......@@ -138,7 +135,7 @@
<a class="sourceLine" id="cb4-25" data-line-number="25"> <span class="kw">cat</span>(<span class="st">"Adjusting covariates:"</span>,<span class="st">"</span><span class="ch">\n</span><span class="st">"</span>)</a>
<a class="sourceLine" id="cb4-26" data-line-number="26"> names &lt;-<span class="st"> </span><span class="kw">strsplit</span>(<span class="dt">x=</span><span class="kw">colnames</span>(exons),<span class="dt">split=</span><span class="st">"_"</span>) <span class="co"># exon names</span></a>
<a class="sourceLine" id="cb4-27" data-line-number="27"> length &lt;-<span class="st"> </span><span class="kw">sapply</span>(names,<span class="cf">function</span>(x) <span class="kw">as.integer</span>(x[[<span class="dv">3</span>]])<span class="op">-</span><span class="kw">as.integer</span>(x[[<span class="dv">2</span>]])) <span class="co"># exon length</span></a>
<a class="sourceLine" id="cb4-28" data-line-number="28"> exons &lt;-<span class="st"> </span>spliceQTL<span class="op">::</span><span class="kw"><a href="http://www.rdocumentation.org/packages/spliceQTL/topics/adjust.covariates">adjust.covariates</a></span>(<span class="dt">x=</span>exons,<span class="dt">group=</span>gene_id,<span class="dt">offset=</span>length) <span class="co"># slow!</span></a>
<a class="sourceLine" id="cb4-28" data-line-number="28"> exons &lt;-<span class="st"> </span>spliceQTL<span class="op">::</span><span class="kw"><a href="http://www.rdocumentation.org/packages/spliceQTL/topics/adjust.variables">adjust.variables</a></span>(<span class="dt">x=</span>exons,<span class="dt">group=</span>gene_id,<span class="dt">offset=</span>length) <span class="co"># slow!</span></a>
<a class="sourceLine" id="cb4-29" data-line-number="29"> </a>
<a class="sourceLine" id="cb4-30" data-line-number="30"> <span class="co"># subset chromosome</span></a>
<a class="sourceLine" id="cb4-31" data-line-number="31"> cond &lt;-<span class="st"> </span><span class="kw">sapply</span>(<span class="kw">strsplit</span>(<span class="dt">x=</span><span class="kw">colnames</span>(exons),<span class="dt">split=</span><span class="st">"_"</span>),<span class="cf">function</span>(x) x[[<span class="dv">1</span>]]<span class="op">==</span>chr)</a>
......
......@@ -78,10 +78,7 @@
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......@@ -2,6 +2,5 @@ pandoc: 2.1.3
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......@@ -81,10 +81,7 @@
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......@@ -6,7 +6,7 @@
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......@@ -28,7 +28,7 @@
<meta property="og:title" content="Adjust exon length — adjust.covariates" />
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<meta property="og:description" content="This function adjusts exon expression data for different exon lengths." />
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......@@ -81,10 +81,7 @@
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......@@ -114,7 +111,7 @@
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<h1>Adjust exon length</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>adjust.covariates.Rd</code></div>
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......@@ -123,7 +120,7 @@
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<pre class="usage"><span class='fu'>adjust.covariates</span>(<span class='no'>x</span>, <span class='no'>offset</span>, <span class='no'>group</span>)</pre>
<pre class="usage"><span class='fu'>adjust.variables</span>(<span class='no'>x</span>, <span class='no'>offset</span>, <span class='no'>group</span>)</pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
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......
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......@@ -88,10 +88,7 @@ retains exons on the autosomes" />
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......@@ -84,10 +84,7 @@ extracts corresponding gene names" />
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......@@ -86,10 +86,7 @@ fuses data from multiple biobanks/technologies" />
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......@@ -86,10 +86,7 @@ changes sample identifiers" />
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......@@ -156,12 +153,6 @@
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<td><p>Adjust library sizes</p></td>
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<td><p>Adjust exon length</p></td>
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......@@ -210,6 +201,12 @@
<p><code><a href="spliceQTL-package.html">spliceQTL-package</a></code> </p>
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<td><p>Alternative Splicing</p></td>
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......@@ -83,10 +83,7 @@ and brings samples into the same order." />
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......@@ -83,10 +83,7 @@ Some functions only work on the virtual machine (see below)." />
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......@@ -139,7 +136,7 @@ Some functions only work on the virtual machine (see below).</p>
<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>
<li><p><code><a href='adjust.covariates.html'>adjust.covariates</a></code></p></li>
<li><p><code>adjust.covariates</code></p></li>
</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>
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% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/functions.R
\name{adjust.covariates}
\alias{adjust.covariates}
\name{adjust.variables}
\alias{adjust.variables}
\title{Adjust exon length}
\usage{
adjust.covariates(x, offset, group)
adjust.variables(x, offset, group)
}
\arguments{
\item{x}{matrix with \eqn{n} rows (samples) and \eqn{p} columns (exons)}
......
---
title: code
title: rainbow (code)
output: rmarkdown::html_vignette
vignette: >
%\VignetteIndexEntry{vignette}
......@@ -37,7 +37,7 @@ spliceQTL::get.exons.geuvadis(path=path)
spliceQTL::get.exons.bbmri(path=path)
```
On the virtual machine, execute this chunk to prepare the data. See the documentation of the R package spliceQTL for further information. (It seems that lme4::lmer in spliceQTL::adjust.covariates fails to release memory. Restart R after each chromosome.)
On the virtual machine, execute this chunk to prepare the data. See the documentation of the R package spliceQTL for further information. (It seems that lme4::lmer in spliceQTL::adjust.variables fails to release memory. Restart R after each chromosome.)
```{r prepare,eval=FALSE}
for(chr in 1:22){
......@@ -67,7 +67,7 @@ for(chr in 1:22){
cat("Adjusting covariates:","\n")
names <- strsplit(x=colnames(exons),split="_") # exon names
length <- sapply(names,function(x) as.integer(x[[3]])-as.integer(x[[2]])) # exon length
exons <- spliceQTL::adjust.covariates(x=exons,group=gene_id,offset=length) # slow!
exons <- spliceQTL::adjust.variables(x=exons,group=gene_id,offset=length) # slow!
# subset chromosome
cond <- sapply(strsplit(x=colnames(exons),split="_"),function(x) x[[1]]==chr)
......
---
title: text
output: rmarkdown::html_vignette
vignette: >
%\VignetteIndexEntry{vignette}
%\VignetteEngine{knitr::rmarkdown}
%\VignetteEncoding{UTF-8}
---
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