Gitlab migration complete. If you have any issue please read the FAQ.

Commit d4e9f3e4 authored by Rauschenberger's avatar Rauschenberger
Browse files

automation

parent 2d00e676
......@@ -48,14 +48,19 @@ NULL
#' Get SNP data (Geuvadis)
#'
#' @description
#' This function transforms SNP data (local machine).
#'
#' This function transforms SNP data (local machine):
#' downloads missing genotype data from ArrayExpress,
#' transforms variant call format to binary files,
#' removes SNPs with low minor allele frequency,
#' labels SNPs in the format "chromosome:position",
#' changes sample identifiers
#'
#' @param chr
#' chromosome: integer \eqn{1-22}
#'
#' @param data
#' local directory for VCF (variant call format)
#' and SDRF (sample and data relationship format) files
#' and SDRF (sample and data relationship format) files;
#'
#' @param path
#' local directory for output
......@@ -94,7 +99,7 @@ get.snps.geuvadis <- function(chr,data=NULL,path=getwd()){
X <- snpStats::read.plink(bed=bed,bim=bim,fam=fam)
X$fam <- NULL; all(diff(X$map$position) > 0)
# fitler MAF
# filter MAF
maf <- snpStats::col.summary(X$genotypes)$MAF
cond <- maf >= 0.05
X$genotypes <- X$genotypes[,cond]
......@@ -120,7 +125,12 @@ get.snps.geuvadis <- function(chr,data=NULL,path=getwd()){
#' Get SNP data (BBMRI)
#'
#' @description
#' This function transforms SNP data (virtual machine).
#' This function transforms SNP data (virtual machine):
#' limits analysis to specified biobanks,
#' reads in genotype data in chunks,
#' removes SNPs with missing values (multiple biobanks/technologies),
#' removes SNPs with low minor allele frequency,
#' fuses data from multiple biobanks/technologies
#'
#' @param chr
#' chromosome: integer \eqn{1-22}
......@@ -207,7 +217,7 @@ get.snps.bbmri <- function(chr,biobank=NULL,path=getwd(),size=500*10^3){
cond <- rowSums(do.call(what="cbind",args=maf))/sum(num)>0.05
if(sum(cond)==0){if(final){break}else{next}}
# Filtering out genotypes.
# Extracting genotypes.
for(j in seq_along(study)){
gt <- vcfR::extract.gt(collect[i,j][[1]][cond,])
gt[gt=="0|0"] <- 0
......@@ -256,7 +266,10 @@ get.snps.bbmri <- function(chr,biobank=NULL,path=getwd(),size=500*10^3){
#' Get exon data (Geuvadis)
#'
#' @description
#' This function transforms exon data (virtual machine).
#' This function transforms exon data (virtual machine):
#' retains exons on the autosomes,
#' labels exons in the format "chromosome_start_end",
#' extracts corresponding gene names
#'
#' @param path
#' data directory
......@@ -283,7 +296,14 @@ get.exons.geuvadis <- function(path=getwd()){
#' Get exon data (BBMRI)
#'
#' @description
#' This function transforms exon data (virtual machine).
#' This function transforms exon data (virtual machine):
#' loads quality controlled gene expression data,
#' extracts sample identifiers,
#' removes samples without SNP data,
#' loads exon expression data,
#' extracts sample identifiers,
#' retains samples that passed quality control,
#' retains exons on the autosomes
#'
#' @param path
#' data directory
......@@ -550,7 +570,7 @@ map.genes <- function(chr,path=getwd(),release="GRCh37",build=71){
#' Search for exons
#'
#' @description
#' This function
#' This function attributes exons to genes.
#'
#' @param gene
#' gene names\strong{:} vector with one entry per gene,
......@@ -590,7 +610,7 @@ map.exons <- function(gene,exon){
#' Search for SNPs
#'
#' @description
#' This function
#' This function attributes SNPs to genes.
#'
#' @param gene.chr
#' chromosome\strong{:}
......@@ -658,7 +678,7 @@ map.snps <- function(gene.chr,gene.start,gene.end,snp.chr,snp.pos,dist=10^3){
#' Drop trivial tests
#'
#' @description
#' This function
#' This function trops trivial tests.
#'
#' @param map
#' list with names "genes", "exons", and "snps"
......
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
<html>
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>Articles • spliceQTL</title>
<!-- jquery -->
<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
<!-- Bootstrap -->
<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
<!-- clipboard.js -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
<script src="../jquery.sticky-kit.min.js"></script>
<script src="../pkgdown.js"></script>
<meta property="og:title" content="Articles" />
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
<![endif]-->
</head>
<body>
<div class="container template-article-index">
<header>
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
<button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">spliceQTL</a>
<span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.0.0</span>
</span>
</div>
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
<a href="../index.html">
<span class="fa fa-home fa-lg"></span>
</a>
</li>
<li>
<a href="../reference/index.html">Reference</a>
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
Articles
<span class="caret"></span>
</a>
<ul class="dropdown-menu" role="menu">
<li>
<a href="../articles/vignette.html">spliceQTL</a>
</li>
</ul>
</li>
<li>
<a href="../news/index.html">Changelog</a>
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/rauschenberger/spliceQTL">
<span class="fa fa-github fa-lg"></span>
</a>
</li>
</ul>
</div><!--/.nav-collapse -->
</div><!--/.container -->
</div><!--/.navbar -->
</header>
<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
<h1>Articles</h1>
</div>
<div class="section ">
<h3>All vignettes</h3>
<p class="section-desc"></p>
<ul>
<li><a href="vignette.html">spliceQTL</a></li>
</ul>
</div>
</div>
</div>
<footer>
<div class="copyright">
<p>Developed by Armin Rauschenberger, Renee Menezes.</p>
</div>
<div class="pkgdown">
<p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
</div>
</footer>
</div>
</body>
</html>
This diff is collapsed.
......@@ -70,18 +70,6 @@
<li>
<a href="reference/index.html">Reference</a>
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
Articles
<span class="caret"></span>
</a>
<ul class="dropdown-menu" role="menu">
<li>
<a href="articles/vignette.html">spliceQTL</a>
</li>
</ul>
</li>
<li>
<a href="news/index.html">Changelog</a>
</li>
......
......@@ -44,18 +44,6 @@
<li>
<a href="reference/index.html">Reference</a>
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
Articles
<span class="caret"></span>
</a>
<ul class="dropdown-menu" role="menu">
<li>
<a href="articles/vignette.html">spliceQTL</a>
</li>
</ul>
</li>
<li>
<a href="news/index.html">Changelog</a>
</li>
......
......@@ -70,18 +70,6 @@
<li>
<a href="../reference/index.html">Reference</a>
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
Articles
<span class="caret"></span>
</a>
<ul class="dropdown-menu" role="menu">
<li>
<a href="../articles/vignette.html">spliceQTL</a>
</li>
</ul>
</li>
<li>
<a href="../news/index.html">Changelog</a>
</li>
......
pandoc: 2.1.3
pkgdown: 1.0.0
pkgdown_sha: d43ca38c74827d1d6babc3a80d48cd3a8e8fad8c
articles:
vignette: vignette.html
articles: {}
......@@ -73,18 +73,6 @@
<li>
<a href="../reference/index.html">Reference</a>
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
Articles
<span class="caret"></span>
</a>
<ul class="dropdown-menu" role="menu">
<li>
<a href="../articles/vignette.html">spliceQTL</a>
</li>
</ul>
</li>
<li>
<a href="../news/index.html">Changelog</a>
</li>
......
......@@ -73,18 +73,6 @@
<li>
<a href="../reference/index.html">Reference</a>
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
Articles
<span class="caret"></span>
</a>
<ul class="dropdown-menu" role="menu">
<li>
<a href="../articles/vignette.html">spliceQTL</a>
</li>
</ul>
</li>
<li>
<a href="../news/index.html">Changelog</a>
</li>
......
......@@ -30,7 +30,7 @@
<meta property="og:title" content="Drop trivial tests — drop.trivial" />
<meta property="og:description" content="This function" />
<meta property="og:description" content="This function trops trivial tests." />
<meta name="twitter:card" content="summary" />
......@@ -73,18 +73,6 @@
<li>
<a href="../reference/index.html">Reference</a>
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
Articles
<span class="caret"></span>
</a>
<ul class="dropdown-menu" role="menu">
<li>
<a href="../articles/vignette.html">spliceQTL</a>
</li>
</ul>
</li>
<li>
<a href="../news/index.html">Changelog</a>
</li>
......@@ -116,7 +104,7 @@
<div class="ref-description">
<p>This function</p>
<p>This function trops trivial tests.</p>
</div>
......
......@@ -30,7 +30,14 @@
<meta property="og:title" content="Get exon data (BBMRI) — get.exons.bbmri" />
<meta property="og:description" content="This function transforms exon data (virtual machine)." />
<meta property="og:description" content="This function transforms exon data (virtual machine):
loads quality controlled gene expression data,
extracts sample identifiers,
removes samples without SNP data,
loads exon expression data,
extracts sample identifiers,
retains samples that passed quality control,
retains exons on the autosomes" />
<meta name="twitter:card" content="summary" />
......@@ -73,18 +80,6 @@
<li>
<a href="../reference/index.html">Reference</a>
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
Articles
<span class="caret"></span>
</a>
<ul class="dropdown-menu" role="menu">
<li>
<a href="../articles/vignette.html">spliceQTL</a>
</li>
</ul>
</li>
<li>
<a href="../news/index.html">Changelog</a>
</li>
......@@ -116,7 +111,14 @@
<div class="ref-description">
<p>This function transforms exon data (virtual machine).</p>
<p>This function transforms exon data (virtual machine):
loads quality controlled gene expression data,
extracts sample identifiers,
removes samples without SNP data,
loads exon expression data,
extracts sample identifiers,
retains samples that passed quality control,
retains exons on the autosomes</p>
</div>
......
......@@ -30,7 +30,10 @@
<meta property="og:title" content="Get exon data (Geuvadis) — get.exons.geuvadis" />
<meta property="og:description" content="This function transforms exon data (virtual machine)." />
<meta property="og:description" content="This function transforms exon data (virtual machine):
retains exons on the autosomes,
labels exons in the format "chromosome_start_end",
extracts corresponding gene names" />
<meta name="twitter:card" content="summary" />
......@@ -73,18 +76,6 @@
<li>
<a href="../reference/index.html">Reference</a>
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
Articles
<span class="caret"></span>
</a>
<ul class="dropdown-menu" role="menu">
<li>
<a href="../articles/vignette.html">spliceQTL</a>
</li>
</ul>
</li>
<li>
<a href="../news/index.html">Changelog</a>
</li>
......@@ -116,7 +107,10 @@
<div class="ref-description">
<p>This function transforms exon data (virtual machine).</p>
<p>This function transforms exon data (virtual machine):
retains exons on the autosomes,
labels exons in the format "chromosome_start_end",
extracts corresponding gene names</p>
</div>
......
......@@ -30,7 +30,12 @@
<meta property="og:title" content="Get SNP data (BBMRI) — get.snps.bbmri" />
<meta property="og:description" content="This function transforms SNP data (virtual machine)." />
<meta property="og:description" content="This function transforms SNP data (virtual machine):
limits analysis to specified biobanks,
reads in genotype data in chunks,
removes SNPs with missing values (multiple biobanks/technologies),
removes SNPs with low minor allele frequency,
fuses data from multiple biobanks/technologies" />
<meta name="twitter:card" content="summary" />
......@@ -73,18 +78,6 @@
<li>
<a href="../reference/index.html">Reference</a>
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
Articles
<span class="caret"></span>
</a>
<ul class="dropdown-menu" role="menu">
<li>
<a href="../articles/vignette.html">spliceQTL</a>
</li>
</ul>
</li>
<li>
<a href="../news/index.html">Changelog</a>
</li>
......@@ -116,7 +109,12 @@
<div class="ref-description">
<p>This function transforms SNP data (virtual machine).</p>
<p>This function transforms SNP data (virtual machine):
limits analysis to specified biobanks,
reads in genotype data in chunks,
removes SNPs with missing values (multiple biobanks/technologies),
removes SNPs with low minor allele frequency,
fuses data from multiple biobanks/technologies</p>
</div>
......
......@@ -30,7 +30,12 @@
<meta property="og:title" content="Get SNP data (Geuvadis) — get.snps.geuvadis" />
<meta property="og:description" content="This function transforms SNP data (local machine)." />
<meta property="og:description" content="This function transforms SNP data (local machine):
downloads missing genotype data from ArrayExpress,
transforms variant call format to binary files,
removes SNPs with low minor allele frequency,
labels SNPs in the format "chromosome:position",
changes sample identifiers" />
<meta name="twitter:card" content="summary" />
......@@ -73,18 +78,6 @@
<li>
<a href="../reference/index.html">Reference</a>
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
Articles
<span class="caret"></span>
</a>
<ul class="dropdown-menu" role="menu">
<li>
<a href="../articles/vignette.html">spliceQTL</a>
</li>
</ul>
</li>
<li>
<a href="../news/index.html">Changelog</a>
</li>
......@@ -116,7 +109,12 @@
<div class="ref-description">
<p>This function transforms SNP data (local machine).</p>
<p>This function transforms SNP data (local machine):
downloads missing genotype data from ArrayExpress,
transforms variant call format to binary files,
removes SNPs with low minor allele frequency,
labels SNPs in the format "chromosome:position",
changes sample identifiers</p>
</div>
......@@ -132,7 +130,7 @@
<tr>
<th>data</th>
<td><p>local directory for VCF (variant call format)
and SDRF (sample and data relationship format) files</p></td>
and SDRF (sample and data relationship format) files;</p></td>
</tr>
<tr>
<th>path</th>
......
......@@ -70,18 +70,6 @@
<li>
<a href="../reference/index.html">Reference</a>
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
Articles
<span class="caret"></span>
</a>
<ul class="dropdown-menu" role="menu">
<li>
<a href="../articles/vignette.html">spliceQTL</a>
</li>
</ul>
</li>
<li>
<a href="../news/index.html">Changelog</a>
</li>
......
......@@ -30,7 +30,7 @@
<meta property="og:title" content="Search for exons — map.exons" />
<meta property="og:description" content="This function" />
<meta property="og:description" content="This function attributes exons to genes." />
<meta name="twitter:card" content="summary" />
......@@ -73,18 +73,6 @@
<li>
<a href="../reference/index.html">Reference</a>
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
Articles
<span class="caret"></span>