Commit ea683705 authored by Rauschenberger's avatar Rauschenberger
Browse files

automation

parent d05acde4
......@@ -83,10 +83,7 @@ and brings samples into the same order." />
</a>
<ul class="dropdown-menu" role="menu">
<li>
<a href="../articles/text.html">text</a>
</li>
<li>
<a href="../articles/code.html">code</a>
<a href="../articles/code.html">rainbow (code)</a>
</li>
</ul>
</li>
......
......@@ -83,10 +83,7 @@ Some functions only work on the virtual machine (see below)." />
</a>
<ul class="dropdown-menu" role="menu">
<li>
<a href="../articles/text.html">text</a>
</li>
<li>
<a href="../articles/code.html">code</a>
<a href="../articles/code.html">rainbow (code)</a>
</li>
</ul>
</li>
......@@ -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>
......
......@@ -81,10 +81,7 @@
</a>
<ul class="dropdown-menu" role="menu">
<li>
<a href="../articles/text.html">text</a>
</li>
<li>
<a href="../articles/code.html">code</a>
<a href="../articles/code.html">rainbow (code)</a>
</li>
</ul>
</li>
......
......@@ -81,10 +81,7 @@
</a>
<ul class="dropdown-menu" role="menu">
<li>
<a href="../articles/text.html">text</a>
</li>
<li>
<a href="../articles/code.html">code</a>
<a href="../articles/code.html">rainbow (code)</a>
</li>
</ul>
</li>
......
% 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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