<p>This vignette requires both a local machine and the BBMRI virtual machine. On the virtual machine, execute this chunk to set the library path, update the R package spliceQTL, and set the working directory.</p>
<p>On the virtual machine, execute this chunk to obtain the BBMRI SNP data, the Geuvadis exon data, and the BBMRI exon data. Choose one out of the six biobanks (CODAM, LL, LLS, NTR, PAN, RS).</p>
<p>On the virtual machine, execute this chunk to test for alternative splicing. See the documentation of the R package spliceQTL for further information.</p>
<aclass="sourceLine"id="cb4-16"data-line-number="16"> list <-<spanclass="st"></span>spliceQTL<spanclass="op">::</span><spanclass="kw"><ahref="http://www.rdocumentation.org/packages/spliceQTL/topics/match.samples">match.samples</a></span>(exons,snps)</a>
<aclass="sourceLine"id="cb5-4"data-line-number="4"> a <-<spanclass="st"></span>pvalue; pvalue <-<spanclass="st"></span><spanclass="ot">NA</span></a>
<aclass="sourceLine"id="cb5-6"data-line-number="6"> b <-<spanclass="st"></span>pvalue; pvalue <-<spanclass="st"></span><spanclass="ot">NA</span></a>
<aclass="sourceLine"id="cb5-11"data-line-number="11"> a <-<spanclass="st"></span>stats<spanclass="op">::</span><spanclass="kw"><ahref="http://www.rdocumentation.org/packages/stats/topics/p.adjust">p.adjust</a></span>(a[names,<spanclass="dv">1</span>])<spanclass="op"><</span><spanclass="fl">0.05</span></a>
<aclass="sourceLine"id="cb5-12"data-line-number="12"> b <-<spanclass="st"></span>stats<spanclass="op">::</span><spanclass="kw"><ahref="http://www.rdocumentation.org/packages/stats/topics/p.adjust">p.adjust</a></span>(b[names,<spanclass="dv">1</span>])<spanclass="op"><</span><spanclass="fl">0.05</span></a>
This vignette requires both a local machine and the BBMRI virtual machine. On the virtual machine, execute this chunk to set the library path, update the R package spliceQTL, and set the working directory.
On the virtual machine, execute this chunk to obtain the BBMRI SNP data, the Geuvadis exon data, and the BBMRI exon data. Choose one out of the six biobanks (CODAM, LL, LLS, NTR, PAN, RS).