automation

docs/reference/match.samples.html

@@ -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>

docs/reference/spliceQTL-package.html

@@ -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>

docs/reference/test.multiple.html

@@ -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>

docs/reference/test.single.html

@@ -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>

man/adjust.covariates.Rd → man/adjust.variables.Rd

 % 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)}

vignettes/code.Rmd

 ---
-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)

vignettes/text.Rmd

----
-title: text
-output: rmarkdown::html_vignette
-vignette: >
-  %\VignetteIndexEntry{vignette}
-  %\VignetteEngine{knitr::rmarkdown}
-  %\VignetteEncoding{UTF-8}
----