Commit 3944a1ae authored by Rauschenberger's avatar Rauschenberger
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automation

parent 30d4f58c
#' @name spliceQTL-package
#' @md
#' @aliases spliceQTL
#'
#' @title
#'
#' Alternative Splicing
#'
#' @description
#'
#' This R package includes various functions
#' for applying the global test of alternative splicing.
#' Some functions only work on the virtual machine (see below).
#'
#' @seealso
#'
#' Prepare BBMRI and Geuvadis data:
#' * \code{\link{get.snps.geuvadis}} (not VM)
#' * \code{\link{get.snps.bbmri}} (only VM)
#' * \code{\link{get.exons.geuvadis}} (only VM)
#' * \code{\link{get.exons.bbmri}} (only VM)
#'
#' Process samples and covariates:
#' * \code{\link{match.samples}}
#' * \code{\link{adjust.samples}}
#' * \code{\link{adjust.covariates}}
#'
#' Search for exons and SNPs:
#' * \code{\link{map.genes}}
#' * \code{\link{map.exons}}
#' * \code{\link{map.snps}}
#' * \code{\link{drop.trivial}}
#'
#' Test for alternative splicing:
#' * \code{\link{test.single}}
#' * \code{\link{test.multiple}}
#'
#' @keywords documentation
#' @docType package
#'
NULL
#' @export #' @export
#' @title #' @title
#' Get SNP data (Geuvadis) #' Get SNP data (Geuvadis)
...@@ -211,6 +255,8 @@ get.snps.bbmri <- function(chr,biobank=NULL,path=getwd(),size=500*10^3){ ...@@ -211,6 +255,8 @@ get.snps.bbmri <- function(chr,biobank=NULL,path=getwd(),size=500*10^3){
} }
#' @export #' @export
#' @title #' @title
#' Get exon data (Geuvadis) #' Get exon data (Geuvadis)
...@@ -617,7 +663,8 @@ map.snps <- function(gene.chr,gene.start,gene.end,snp.chr,snp.pos,dist=10^3){ ...@@ -617,7 +663,8 @@ map.snps <- function(gene.chr,gene.start,gene.end,snp.chr,snp.pos,dist=10^3){
#' #'
#' @param map #' @param map
#' list with names "genes", "exons", and "snps" #' list with names "genes", "exons", and "snps"
#' (output from \code{map.genes}, \code{map.exons}, and \code{map.snps}) #' (output from \code{\link{map.genes}}, \code{\link{map.exons}},
#' and \code{\link{map.snps}})
#' #'
#' @details #' @details
#' This functions drops tests for genes without SNPs or with a single exon. #' This functions drops tests for genes without SNPs or with a single exon.
...@@ -684,7 +731,8 @@ drop.trivial <- function(map){ ...@@ -684,7 +731,8 @@ drop.trivial <- function(map){
#' #'
#' @param map #' @param map
#' list with names "genes", "exons", and "snps" #' list with names "genes", "exons", and "snps"
#' (output from \code{map.genes}, \code{map.exons}, and \code{map.snps}) #' (output from \code{\link{map.genes}}, \code{\link{map.exons}},
#' and \code{\link{map.snps}})
#' #'
#' @param i #' @param i
#' gene index\strong{:} #' gene index\strong{:}
......
...@@ -128,7 +128,8 @@ ...@@ -128,7 +128,8 @@
<tr> <tr>
<th>map</th> <th>map</th>
<td><p>list with names "genes", "exons", and "snps" <td><p>list with names "genes", "exons", and "snps"
(output from <code>map.genes</code>, <code>map.exons</code>, and <code>map.snps</code>)</p></td> (output from <code><a href='map.genes.html'>map.genes</a></code>, <code><a href='map.exons.html'>map.exons</a></code>,
and <code><a href='map.snps.html'>map.snps</a></code>)</p></td>
</tr> </tr>
</table> </table>
......
...@@ -201,6 +201,12 @@ ...@@ -201,6 +201,12 @@
<p><code><a href="get.exons.bbmri.html">get.exons.bbmri()</a></code> </p> <p><code><a href="get.exons.bbmri.html">get.exons.bbmri()</a></code> </p>
</td> </td>
<td><p>Get exon data (BBMRI)</p></td> <td><p>Get exon data (BBMRI)</p></td>
</tr><tr>
<!-- -->
<td>
<p><code><a href="spliceQTL-package.html">spliceQTL-package</a></code> </p>
</td>
<td><p>Alternative Splicing</p></td>
</tr> </tr>
</tbody> </tbody>
</table> </table>
......
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for applying the global test of alternative splicing.
Some functions only work on the virtual machine (see below)." />
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<h1>Alternative Splicing</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>spliceQTL-package.Rd</code></div>
</div>
<div class="ref-description">
<p>This R package includes various functions
for applying the global test of alternative splicing.
Some functions only work on the virtual machine (see below).</p>
</div>
<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
<div class='dont-index'><p>Prepare BBMRI and Geuvadis data:</p><ul>
<li><p><code><a href='get.snps.geuvadis.html'>get.snps.geuvadis</a></code> (not VM)</p></li>
<li><p><code><a href='get.snps.bbmri.html'>get.snps.bbmri</a></code> (only VM)</p></li>
<li><p><code><a href='get.exons.geuvadis.html'>get.exons.geuvadis</a></code> (only VM)</p></li>
<li><p><code><a href='get.exons.bbmri.html'>get.exons.bbmri</a></code> (only VM)</p></li>
</ul></div>
<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>
</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>
<li><p><code><a href='map.exons.html'>map.exons</a></code></p></li>
<li><p><code><a href='map.snps.html'>map.snps</a></code></p></li>
<li><p><code><a href='drop.trivial.html'>drop.trivial</a></code></p></li>
</ul></div>
<div class='dont-index'><p>Test for alternative splicing:</p><ul>
<li><p><code><a href='test.single.html'>test.single</a></code></p></li>
<li><p><code><a href='test.multiple.html'>test.multiple</a></code></p></li>
</ul></div>
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<li><a href="#see-also">See also</a></li>
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...@@ -138,7 +138,8 @@ matrix with \(n\) rows (samples) and \(q\) columns (SNPs)</p></td> ...@@ -138,7 +138,8 @@ matrix with \(n\) rows (samples) and \(q\) columns (SNPs)</p></td>
<tr> <tr>
<th>map</th> <th>map</th>
<td><p>list with names "genes", "exons", and "snps" <td><p>list with names "genes", "exons", and "snps"
(output from <code>map.genes</code>, <code>map.exons</code>, and <code>map.snps</code>)</p></td> (output from <code><a href='map.genes.html'>map.genes</a></code>, <code><a href='map.exons.html'>map.exons</a></code>,
and <code><a href='map.snps.html'>map.snps</a></code>)</p></td>
</tr> </tr>
<tr> <tr>
<th>i</th> <th>i</th>
......
...@@ -8,7 +8,8 @@ drop.trivial(map) ...@@ -8,7 +8,8 @@ drop.trivial(map)
} }
\arguments{ \arguments{
\item{map}{list with names "genes", "exons", and "snps" \item{map}{list with names "genes", "exons", and "snps"
(output from \code{map.genes}, \code{map.exons}, and \code{map.snps})} (output from \code{\link{map.genes}}, \code{\link{map.exons}},
and \code{\link{map.snps}})}
} }
\description{ \description{
This function This function
......
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/functions.R
\docType{package}
\name{spliceQTL-package}
\alias{spliceQTL-package}
\alias{spliceQTL}
\title{Alternative Splicing}
\description{
This R package includes various functions
for applying the global test of alternative splicing.
Some functions only work on the virtual machine (see below).
}
\seealso{
Prepare BBMRI and Geuvadis data:
\itemize{
\item \code{\link{get.snps.geuvadis}} (not VM)
\item \code{\link{get.snps.bbmri}} (only VM)
\item \code{\link{get.exons.geuvadis}} (only VM)
\item \code{\link{get.exons.bbmri}} (only VM)
}
Process samples and covariates:
\itemize{
\item \code{\link{match.samples}}
\item \code{\link{adjust.samples}}
\item \code{\link{adjust.covariates}}
}
Search for exons and SNPs:
\itemize{
\item \code{\link{map.genes}}
\item \code{\link{map.exons}}
\item \code{\link{map.snps}}
\item \code{\link{drop.trivial}}
}
Test for alternative splicing:
\itemize{
\item \code{\link{test.single}}
\item \code{\link{test.multiple}}
}
}
\keyword{documentation}
...@@ -14,7 +14,8 @@ matrix with \eqn{n} rows (samples) and \eqn{p} columns (exons)} ...@@ -14,7 +14,8 @@ matrix with \eqn{n} rows (samples) and \eqn{p} columns (exons)}
matrix with \eqn{n} rows (samples) and \eqn{q} columns (SNPs)} matrix with \eqn{n} rows (samples) and \eqn{q} columns (SNPs)}
\item{map}{list with names "genes", "exons", and "snps" \item{map}{list with names "genes", "exons", and "snps"
(output from \code{map.genes}, \code{map.exons}, and \code{map.snps})} (output from \code{\link{map.genes}}, \code{\link{map.exons}},
and \code{\link{map.snps}})}
\item{i}{gene index\strong{:} \item{i}{gene index\strong{:}
integer between \eqn{1} and \code{nrow(map$genes)}} integer between \eqn{1} and \code{nrow(map$genes)}}
......
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