automation

R/function.R

@@ -63,20 +63,26 @@ prepare.data.matrices <- function(Y,X){
 #' @description
 #' This function adjusts exon expression data for different library sizes.
 #' 
-#' @param y
+#' @param Y
 #' matrix with \eqn{n} rows (samples) and \eqn{p} columns (exons)
 #' 
 #' @examples
 #' NA
 #' 
-adjust.library.sizes <- function(y){
-    n <- nrow(y); p <- ncol(y)
-    lib.size <- rowSums(y)
-    norm.factors <- edgeR::calcNormFactors(object=t(y),lib.size=lib.size)
+adjust.library.sizes <- function(Y){
+    if(!is.matrix(Y)){
+        stop("Argument Y is no matrix.",call.=FALSE)
+    }
+    if(!is.numeric(Y)){
+        stop("Argument Y is not numeric.",call.=FALSE)
+    }
+    n <- nrow(Y); p <- ncol(Y)
+    lib.size <- rowSums(Y)
+    norm.factors <- edgeR::calcNormFactors(object=t(Y),lib.size=lib.size)
     gamma <- norm.factors*lib.size/mean(lib.size)
     gamma <- matrix(gamma,nrow=n,ncol=p,byrow=FALSE)
-    y <- y/gamma
-    return(y)
+    Y <- Y/gamma
+    return(Y)
 }
 
 #' @export
@@ -86,7 +92,7 @@ adjust.library.sizes <- function(y){
 #' @description
 #' This function adjusts exon expression data for different exon lengths.
 #' 
-#' @param y
+#' @param Y
 #' matrix with \eqn{n} rows (samples) and \eqn{p} columns (exons)
 #' 
 #' @param gene
@@ -104,14 +110,23 @@ adjust.library.sizes <- function(y){
 #' @examples
 #' NA
 #' 
-adjust.exon.length <- function(y,gene,start,end){
-    n <- nrow(y); p <- ncol(y); names <- dimnames(y)
-    y <- as.numeric(y)
-    x <- rep(end-start,times=n)
-    gene <- rep(gene,times=n)
-    lmer <- lme4::lmer(y ~ x + (1|gene))
-    y <- matrix(stats::residuals(lmer),nrow=p,ncol=n,dimnames=names)
-    return(y - min(y))
+adjust.exon.length <- function(Y,gene,start,end){
+    if(!is.matrix(Y)){
+        stop("Argument Y is no matrix.",call.=FALSE)
+    }
+    if(any(ncol(Y)!=c(length(gene),length(start),length(end)))){
+        stop("Contradictory dimensions.",call.=FALSE)
+    }
+    n <- nrow(Y); p <- ncol(Y); names <- dimnames(Y)
+    Y <- as.numeric(Y) # wrong?
+    x <- rep(end-start,each=n)
+    gene <- strsplit(gene,split=",")
+    gene <- sapply(gene,function(x) x[[1]][1])
+    gene <- rep(gene,each=n)
+    lmer <- lme4::lmer(Y ~ x + (1|gene))
+    Y <- matrix(stats::residuals(lmer),nrow=n,ncol=p,dimnames=names)
+    Y <- Y-min(Y)
+    return(Y)
 }
 
 #' @export

README.Rmd

@@ -13,17 +13,11 @@ knitr::opts_chunk$set(
 )
 ```
 
-## Scope
-
-spliceQTL
-
-## Installation
 
 ```{r,eval=FALSE}
 #install.packages("devtools")
 devtools::install_github("rauschenberger/spliceQTL")
 ```
 
-## Reference
 
 

README.md

 
 <!-- Modify xxx.Rmd, not xxx.md! -->
 
-## Scope
-
-spliceQTL
-
-## Installation
-
 ``` r
 #install.packages("devtools")
 devtools::install_github("rauschenberger/spliceQTL")
 ```
-
-## Reference

docs/index.html

@@ -83,21 +83,8 @@
     
     
 <!-- Modify xxx.Rmd, not xxx.md! -->
-<div id="scope" class="section level2">
-<h2 class="hasAnchor">
-<a href="#scope" class="anchor"></a>Scope</h2>
-<p>spliceQTL</p>
-</div>
-<div id="installation" class="section level2">
-<h2 class="hasAnchor">
-<a href="#installation" class="anchor"></a>Installation</h2>
 <div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb1-1" data-line-number="1"><span class="co">#install.packages("devtools")</span></a>
 <a class="sourceLine" id="cb1-2" data-line-number="2">devtools<span class="op">::</span><span class="kw"><a href="http://www.rdocumentation.org/packages/devtools/topics/install_github">install_github</a></span>(<span class="st">"rauschenberger/spliceQTL"</span>)</a></code></pre></div>
-</div>
-<div id="reference" class="section level2">
-<h2 class="hasAnchor">
-<a href="#reference" class="anchor"></a>Reference</h2>
-</div>
   </div>
 
   <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">

docs/reference/adjust.exon.length.html

@@ -120,13 +120,13 @@
     
     </div>
 
-    <pre class="usage"><span class='fu'>adjust.exon.length</span>(<span class='no'>y</span>, <span class='no'>gene</span>, <span class='no'>start</span>, <span class='no'>end</span>)</pre>
+    <pre class="usage"><span class='fu'>adjust.exon.length</span>(<span class='no'>Y</span>, <span class='no'>gene</span>, <span class='no'>start</span>, <span class='no'>end</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>y</th>
+      <th>Y</th>
       <td><p>matrix with \(n\) rows (samples) and \(p\) columns (exons)</p></td>
     </tr>
     <tr>

docs/reference/adjust.library.sizes.html

@@ -120,13 +120,13 @@
     
     </div>
 
-    <pre class="usage"><span class='fu'>adjust.library.sizes</span>(<span class='no'>y</span>)</pre>
+    <pre class="usage"><span class='fu'>adjust.library.sizes</span>(<span class='no'>Y</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>y</th>
+      <th>Y</th>
       <td><p>matrix with \(n\) rows (samples) and \(p\) columns (exons)</p></td>
     </tr>
     </table>

man/adjust.exon.length.Rd

@@ -4,10 +4,10 @@
 \alias{adjust.exon.length}
 \title{Adjust exon length}
 \usage{
-adjust.exon.length(y, gene, start, end)
+adjust.exon.length(Y, gene, start, end)
 }
 \arguments{
-\item{y}{matrix with \eqn{n} rows (samples) and \eqn{p} columns (exons)}
+\item{Y}{matrix with \eqn{n} rows (samples) and \eqn{p} columns (exons)}
 
 \item{gene}{gene (not exon) names\strong{:} vector of length \eqn{p}}
 

man/adjust.library.sizes.Rd

@@ -4,10 +4,10 @@
 \alias{adjust.library.sizes}
 \title{Adjust library sizes}
 \usage{
-adjust.library.sizes(y)
+adjust.library.sizes(Y)
 }
 \arguments{
-\item{y}{matrix with \eqn{n} rows (samples) and \eqn{p} columns (exons)}
+\item{Y}{matrix with \eqn{n} rows (samples) and \eqn{p} columns (exons)}
 }
 \description{
 This function adjusts exon expression data for different library sizes.