Commit 49360ff7 authored by Rauschenberger's avatar Rauschenberger
Browse files

automation

parent bd61088d
......@@ -536,7 +536,7 @@ adjust.variables <- function(x,offset,group){
map.genes <- function(chr,path=getwd(),release="GRCh37",build=71){
# check input
if(!chr %in% 1:22){
if((!is.null(chr)) && (!chr %in% 1:22)){
stop("Invalid argument \"chr\".",call.=FALSE)
}
if(!release %in% c("NCBI36","GRCh37","GRCh38")){
......@@ -558,8 +558,12 @@ map.genes <- function(chr,path=getwd(),release="GRCh37",build=71){
refGenome::basedir(object) <- path
refGenome::read.gtf(object,filename=file)
x <- refGenome::getGenePositions(object=object,by="gene_id")
if(is.null(chr)){
x <- x[x$gene_biotype=="protein_coding",]
} else {
x <- x[x$seqid==chr & x$gene_biotype=="protein_coding",]
x <- x[,c("gene_id","seqid","start","end")]
}
x <- x[,c("gene_id","seqid","start","end","gene_name")] # added "gene_name"
rownames(x) <- NULL
colnames(x)[colnames(x)=="seqid"] <- "chr"
return(x)
......
......@@ -182,8 +182,8 @@
<a class="sourceLine" id="cb5-8" data-line-number="8"> }</a>
<a class="sourceLine" id="cb5-9" data-line-number="9">}</a></code></pre></div>
<p>On the virtual machine, execute this chunk to compare the results between the Geuvadis and the BBMRI project.</p>
<div class="sourceCode" id="cb6"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb6-1" data-line-number="1">list &lt;-<span class="st"> </span><span class="kw">list</span>()</a>
<a class="sourceLine" id="cb6-2" data-line-number="2">table &lt;-<span class="st"> </span><span class="kw">data.frame</span>(<span class="dt">chr=</span><span class="kw">seq_len</span>(<span class="dv">22</span>))</a>
<div class="sourceCode" id="cb6"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb6-1" data-line-number="1">table &lt;-<span class="st"> </span><span class="kw">data.frame</span>(<span class="dt">chr=</span><span class="kw">seq_len</span>(<span class="dv">22</span>))</a>
<a class="sourceLine" id="cb6-2" data-line-number="2">list &lt;-<span class="st"> </span><span class="kw">list</span>()</a>
<a class="sourceLine" id="cb6-3" data-line-number="3"><span class="cf">for</span>(i <span class="cf">in</span> <span class="kw">seq_len</span>(<span class="dv">22</span>)){</a>
<a class="sourceLine" id="cb6-4" data-line-number="4"> <span class="co"># load p-values</span></a>
<a class="sourceLine" id="cb6-5" data-line-number="5"> <span class="kw">load</span>(<span class="kw">file.path</span>(path,<span class="kw">paste0</span>(<span class="st">"pval.Geuvadis.chr"</span>,i,<span class="st">".RData"</span>)))</a>
......@@ -228,9 +228,12 @@
<a class="sourceLine" id="cb6-44" data-line-number="44"> list[[i]] &lt;-<span class="st"> </span><span class="kw">data.frame</span>(<span class="dt">chr=</span>i,<span class="dt">gene=</span><span class="kw">names</span>(a),<span class="dt">Geuvadis=</span><span class="dv">1</span><span class="op">*</span>a,<span class="dt">LLS=</span><span class="dv">1</span><span class="op">*</span>b,<span class="dt">row.names=</span><span class="kw">seq_along</span>(a))</a>
<a class="sourceLine" id="cb6-45" data-line-number="45"> </a>
<a class="sourceLine" id="cb6-46" data-line-number="46">}</a>
<a class="sourceLine" id="cb6-47" data-line-number="47">list &lt;-<span class="st"> </span><span class="kw">do.call</span>(<span class="dt">what=</span><span class="st">"rbind"</span>,<span class="dt">args=</span>list)</a>
<a class="sourceLine" id="cb6-48" data-line-number="48"><span class="kw">save</span>(list,<span class="dt">file=</span><span class="st">"list.RData"</span>)</a>
<a class="sourceLine" id="cb6-49" data-line-number="49"><span class="kw">save</span>(table,<span class="dt">file=</span><span class="st">"table.RData"</span>)</a></code></pre></div>
<a class="sourceLine" id="cb6-47" data-line-number="47"><span class="kw">save</span>(table,<span class="dt">file=</span><span class="st">"table.RData"</span>)</a>
<a class="sourceLine" id="cb6-48" data-line-number="48"></a>
<a class="sourceLine" id="cb6-49" data-line-number="49">list &lt;-<span class="st"> </span><span class="kw">do.call</span>(<span class="dt">what=</span><span class="st">"rbind"</span>,<span class="dt">args=</span>list)</a>
<a class="sourceLine" id="cb6-50" data-line-number="50">names &lt;-<span class="st"> </span><span class="kw">do.call</span>(<span class="dt">what=</span><span class="st">"rbind"</span>,<span class="dt">args=</span>list)</a>
<a class="sourceLine" id="cb6-51" data-line-number="51">list<span class="op">$</span>symbol &lt;-<span class="st"> </span>names<span class="op">$</span>gene_name[<span class="kw">match</span>(<span class="dt">x=</span>list<span class="op">$</span>gene,names<span class="op">$</span>gene_id)]</a>
<a class="sourceLine" id="cb6-52" data-line-number="52"><span class="kw">save</span>(list,<span class="dt">file=</span><span class="st">"list.RData"</span>)</a></code></pre></div>
<p>On the virtual machine, execute this chunk to plot correlations between SNPs and exons (unclear which genes should be examined).</p>
<div class="sourceCode" id="cb7"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb7-1" data-line-number="1">data &lt;-<span class="st"> "LLS"</span> <span class="co"># "Geuvadis" or "LLS"</span></a>
<a class="sourceLine" id="cb7-2" data-line-number="2">chr &lt;-<span class="st"> </span><span class="dv">22</span> <span class="co"># 1,2,3,...,22</span></a>
......
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......@@ -119,8 +119,8 @@ for(chr in 22:1){ # 22:1
On the virtual machine, execute this chunk to compare the results between the Geuvadis and the BBMRI project.
```{r,eval=FALSE}
list <- list()
table <- data.frame(chr=seq_len(22))
list <- list()
for(i in seq_len(22)){
# load p-values
load(file.path(path,paste0("pval.Geuvadis.chr",i,".RData")))
......@@ -165,9 +165,12 @@ for(i in seq_len(22)){
list[[i]] <- data.frame(chr=i,gene=names(a),Geuvadis=1*a,LLS=1*b,row.names=seq_along(a))
}
save(table,file="table.RData")
list <- do.call(what="rbind",args=list)
names <- do.call(what="rbind",args=list)
list$symbol <- names$gene_name[match(x=list$gene,names$gene_id)]
save(list,file="list.RData")
save(table,file="table.RData")
```
On the virtual machine, execute this chunk to plot correlations between SNPs and exons (unclear which genes should be examined).
......
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