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<h1 class="title toc-ignore">Overlap Molecular QTLs</h1>
<h4 class="author"><em>Briana Mittleman</em></h4>
<h4 class="date"><em>9/6/2018</em></h4>
</div>
<p><strong>Last updated:</strong> 2018-09-06</p>
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<a href="https://github.com/brimittleman/threeprimeseq/blob/46b7343493337a9c20b5ce490b66cbb942467169/analysis/overlap_qtls.Rmd" target="_blank">46b7343</a>
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Briana Mittleman
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add overlap analysis with code to subset
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<p></details></p>
<hr />
<p>I will use this to overlap my QTLs with the other molecular QTLs already identified in the same individuals. First pass I will subset my nuclear and total nomial qtls by the snps with pvals less than .05 in each of the sets and make a qqplot.</p>
<p>I want to create a python script that takes in which type of qtl and a pvalue and subsets the full file for snps that pass that filter.</p>
<p>subset_qtls.py</p>
<pre class="bash"><code>
def main(inFile, outFile, qtl, cutoff):
fout=open(outFile, "w")
ifile=open(inFile, "r")
cutoff=float(cutoff)
qtl_types= ['4su_30', '4su_60', 'RNAseq', 'RNAseqGeuvadis', 'ribo', 'prot']
if qtl not in qtl_types:
raise NameError("QTL arg must be 4su_30, 4su_60, RNAseq, RNAseqGeuvadis, ribo, or prot")
elif qtl=="4su_30":
target=4
elif qtl=="4su60":
target=5
elif qtl=="RNAseq":
target=6
elif qtl=="RNAseqGeuvadis":
target=7
elif qtl=="ribo":
target =8
elif qtl=="prot":
target=9
for num,ln in enumerate(ifile):
if num > 0 :
line_list = ln.split()
chrom=line_list[0]
pos=line_list[1]
rsid=line_list[2]
geneID=line_list[3]
val = float(line_list[target].split(":")[0])
if val <= cutoff:
fout.write("%s\t%s\t%s\t%s\t%f\n"%(chrom, pos, rsid, geneID,val))
if __name__ == "__main__":
import sys
qtl = sys.argv[1]
cutoff= sys.argv[2]
inFile = "/project2/gilad/briana/threeprimeseq/data/otherQTL/summary_betas_ste_100kb.txt"
outFile = "/project2/gilad/briana/threeprimeseq/data/otherQTL/summary_betas_ste_100kb.%s%s.txt"%(qtl, cutoff)
main(inFile, outFile, qtl, cutoff)</code></pre>
<p>I can run this to subset by each qtl at .05</p>
<p>run_subsetQTLs05.sh</p>
<pre class="bash"><code>#!/bin/bash
#SBATCH --job-name=run_subsetqtl05
#SBATCH --account=pi-yangili1
#SBATCH --time=24:00:00
#SBATCH --output=run_subsetqtl05.out
#SBATCH --error=run_subsetqtl05.err
#SBATCH --partition=broadwl
#SBATCH --mem=12G
#SBATCH --mail-type=END
module load Anaconda3
source activate three-prime-env
qtls=('4su_30', '4su_60', 'RNAseq', 'RNAseqGeuvadis', 'ribo', 'prot')
for i in ${qtls[@]}; do
python subset_qtls.py $i .05
done
</code></pre>
<div id="session-information" class="section level2">
<h2>Session information</h2>
<pre class="r"><code>sessionInfo()</code></pre>
<pre><code>R version 3.5.1 (2018-07-02)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Sierra 10.12.6
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] workflowr_1.1.1 Rcpp_0.12.18 digest_0.6.16
[4] rprojroot_1.3-2 R.methodsS3_1.7.1 backports_1.1.2
[7] git2r_0.23.0 magrittr_1.5 evaluate_0.11
[10] stringi_1.2.4 whisker_0.3-2 R.oo_1.22.0
[13] R.utils_2.7.0 rmarkdown_1.10 tools_3.5.1
[16] stringr_1.3.1 yaml_2.2.0 compiler_3.5.1
[19] htmltools_0.3.6 knitr_1.20 </code></pre>
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