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<h1 class="title toc-ignore">Coverage analysis</h1>
<h4 class="author"><em>Briana Mittleman</em></h4>
<h4 class="date"><em>7/13/2018</em></h4>

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<p><strong>Last updated:</strong> 2018-07-13</p>
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<a href="https://github.com/brimittleman/threeprimeseq/blob/4a847692c90977347c2a192e8e68e1d2d02b6fa5/analysis/cov.analysis.threeprime1.Rmd" target="_blank">4a84769</a>
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Briana Mittleman
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2018-07-13
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add analysis for coparing coverage of RNAseq and 3’ seq
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<p></details></p>
<hr />
<p>I will use this analysis to compare the 3’ seq data to the RNA seq data. I am going to look at the protein coding genes.</p>
<pre class="r"><code>library(workflowr)</code></pre>
<pre><code>Loading required package: rmarkdown</code></pre>
<pre><code>This is workflowr version 1.0.1
Run ?workflowr for help getting started</code></pre>
<pre class="r"><code>library(ggplot2)
library(tidyr)
library(dplyr)</code></pre>
<pre><code>Warning: package &#39;dplyr&#39; was built under R version 3.4.4</code></pre>
<pre><code>
Attaching package: &#39;dplyr&#39;</code></pre>
<pre><code>The following objects are masked from &#39;package:stats&#39;:

    filter, lag</code></pre>
<pre><code>The following objects are masked from &#39;package:base&#39;:

    intersect, setdiff, setequal, union</code></pre>
<pre class="r"><code>library(reshape2)</code></pre>
<pre><code>Warning: package &#39;reshape2&#39; was built under R version 3.4.3</code></pre>
<pre><code>
Attaching package: &#39;reshape2&#39;</code></pre>
<pre><code>The following object is masked from &#39;package:tidyr&#39;:

    smiths</code></pre>
<p>Load RNA seq gene cov for 18486.</p>
<pre class="r"><code>rnaseq=read.table(&quot;../data/18486.genecov.txt&quot;)
names(rnaseq)=c(&quot;Chr&quot;, &quot;start&quot;, &quot;end&quot;, &quot;gene&quot;, &quot;score&quot;, &quot;strand&quot;, &quot;count&quot;)
rnaseq_counts= rnaseq %&gt;% select(gene, count)</code></pre>
<p>Load all total fraction 3’ seq libraries.</p>
<pre class="r"><code>t18486=read.table(&quot;../data/gene_cov/YL-SP-18486-T_S9_R1_001-genecov.txt&quot;,col.names =c(&quot;Chr&quot;, &quot;start&quot;, &quot;end&quot;, &quot;gene&quot;, &quot;score&quot;, &quot;strand&quot;, &quot;T18486&quot;) )
t18497=read.table(&quot;../data/gene_cov/YL-SP-18497-T_S11_R1_001-genecov.txt&quot;,col.names =c(&quot;Chr&quot;, &quot;start&quot;, &quot;end&quot;, &quot;gene&quot;, &quot;score&quot;, &quot;strand&quot;, &quot;T18497&quot;) )
t18500=read.table(&quot;../data/gene_cov/YL-SP-18500-T_S19_R1_001-genecov.txt&quot;,col.names =c(&quot;Chr&quot;, &quot;start&quot;, &quot;end&quot;, &quot;gene&quot;, &quot;score&quot;, &quot;strand&quot;, &quot;T18500&quot;) )
t18505=read.table(&quot;../data/gene_cov/YL-SP-18500-T_S19_R1_001-genecov.txt&quot;,col.names =c(&quot;Chr&quot;, &quot;start&quot;, &quot;end&quot;, &quot;gene&quot;, &quot;score&quot;, &quot;strand&quot;, &quot;T18505&quot;) )
t18508=read.table(&quot;../data/gene_cov/YL-SP-18508-T_S5_R1_001-genecov.txt&quot;,col.names =c(&quot;Chr&quot;, &quot;start&quot;, &quot;end&quot;, &quot;gene&quot;, &quot;score&quot;, &quot;strand&quot;, &quot;T18508&quot;) )
t18853=read.table(&quot;../data/gene_cov/YL-SP-18853-T_S31_R1_001-genecov.txt&quot;,col.names =c(&quot;Chr&quot;, &quot;start&quot;, &quot;end&quot;, &quot;gene&quot;, &quot;score&quot;, &quot;strand&quot;, &quot;T18853&quot;) )
t18870=read.table(&quot;../data/gene_cov/YL-SP-18870-T_S23_R1_001-genecov.txt&quot;,col.names =c(&quot;Chr&quot;, &quot;start&quot;, &quot;end&quot;, &quot;gene&quot;, &quot;score&quot;, &quot;strand&quot;, &quot;T18870&quot;) )
t19128=read.table(&quot;../data/gene_cov/YL-SP-19128-T_S29_R1_001-genecov.txt&quot;,col.names =c(&quot;Chr&quot;, &quot;start&quot;, &quot;end&quot;, &quot;gene&quot;, &quot;score&quot;, &quot;strand&quot;, &quot;T19128&quot;) )
t19141=read.table(&quot;../data/gene_cov/YL-SP-19141-T_S17_R1_001-genecov.txt&quot;,col.names =c(&quot;Chr&quot;, &quot;start&quot;, &quot;end&quot;, &quot;gene&quot;, &quot;score&quot;, &quot;strand&quot;, &quot;T19141&quot;) )
t19193=read.table(&quot;../data/gene_cov/YL-SP-19193-T_S21_R1_001-genecov.txt&quot;,col.names =c(&quot;Chr&quot;, &quot;start&quot;, &quot;end&quot;, &quot;gene&quot;, &quot;score&quot;, &quot;strand&quot;, &quot;T19193&quot;) )
t19209=read.table(&quot;../data/gene_cov/YL-SP-19209-T_S15_R1_001-genecov.txt&quot;,col.names =c(&quot;Chr&quot;, &quot;start&quot;, &quot;end&quot;, &quot;gene&quot;, &quot;score&quot;, &quot;strand&quot;, &quot;T19209&quot;) )
t19223=read.table(&quot;../data/gene_cov/YL-SP-19233-T_S7_R1_001-genecov.txt&quot;,col.names =c(&quot;Chr&quot;, &quot;start&quot;, &quot;end&quot;, &quot;gene&quot;, &quot;score&quot;, &quot;strand&quot;, &quot;T19223&quot;) )
t19225=read.table(&quot;../data/gene_cov/YL-SP-19225-T_S27_R1_001-genecov.txt&quot;,col.names =c(&quot;Chr&quot;, &quot;start&quot;, &quot;end&quot;, &quot;gene&quot;, &quot;score&quot;, &quot;strand&quot;, &quot;T19225&quot;) )
t19238=read.table(&quot;../data/gene_cov/YL-SP-19238-T_S3_R1_001-genecov.txt&quot;,col.names =c(&quot;Chr&quot;, &quot;start&quot;, &quot;end&quot;, &quot;gene&quot;, &quot;score&quot;, &quot;strand&quot;, &quot;T19238&quot;) )
t19239=read.table(&quot;../data/gene_cov/YL-SP-19239-T_S13_R1_001-genecov.txt&quot;,col.names =c(&quot;Chr&quot;, &quot;start&quot;, &quot;end&quot;, &quot;gene&quot;, &quot;score&quot;, &quot;strand&quot;, &quot;T19239&quot;) )
t19257=read.table(&quot;../data/gene_cov/YL-SP-19257-T_S25_R1_001-genecov.txt&quot;,col.names =c(&quot;Chr&quot;, &quot;start&quot;, &quot;end&quot;, &quot;gene&quot;, &quot;score&quot;, &quot;strand&quot;, &quot;T19257&quot;) )</code></pre>
<p>Merge all of the files:</p>
<pre class="r"><code>threeprimeall=cbind(t18486,t18497$T18497, t18500$T18500, t18505$T18505, t18508$T18508, t18853$T18853, t18870$T18870, t19128$T19128, t19141$T19141,t19193$T19193, t19209$T19209, t19223$T19223, t19225$T19225, t19238$T19238, t19239$T19239, t19257$T19257)


threeprimeall_sum=threeprimeall %&gt;% mutate(Counts_all= T18486,t18497$T18497, t18500$T18500, t18505$T18505, t18508$T18508, t18853$T18853, t18870$T18870, t19128$T19128, t19141$T19141,t19193$T19193, t19209$T19209, t19223$T19223, t19225$T19225, t19238$T19238, t19239$T19239, t19257$T19257) %&gt;% select(gene, Counts_all)</code></pre>
<pre><code>Warning: package &#39;bindrcpp&#39; was built under R version 3.4.4</code></pre>
<pre class="r"><code>threeprimeall_sum$gene=as.character(threeprimeall_sum$gene)</code></pre>
<p>Melt the data fro ggplot.</p>
<pre class="r"><code>all_counts= cbind(threeprimeall_sum,rnaseq_counts$count) 
colnames(all_counts)= c(&quot;gene&quot;, &quot;threeprime&quot;, &quot;RNAseq&quot;)

all_counts_melt= melt(all_counts, id.vars=&quot;gene&quot;)
names(all_counts_melt)=c(&quot;gene&quot;, &quot;Library&quot;, &quot;Count&quot;)</code></pre>
<p>Plot the CDFs</p>
<pre class="r"><code>ggplot(all_counts_melt, aes(x=log10(Count), col=Library)) + stat_ecdf(geom = &quot;step&quot;, pad = FALSE) + labs(title= &quot;Log10 counts CDF&quot;)</code></pre>
<pre><code>Warning: Removed 9859 rows containing non-finite values (stat_ecdf).</code></pre>
<p><img src="figure/cov.analysis.threeprime1.Rmd/unnamed-chunk-6-1.png" width="672" style="display: block; margin: auto;" /></p>
<div id="session-information" class="section level2">
<h2>Session information</h2>
<pre class="r"><code>sessionInfo()</code></pre>
<pre><code>R version 3.4.2 (2017-09-28)
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/3.4/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.4/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     

other attached packages:
[1] bindrcpp_0.2.2  reshape2_1.4.3  dplyr_0.7.5     tidyr_0.7.2    
[5] ggplot2_2.2.1   workflowr_1.0.1 rmarkdown_1.8.5

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.17      compiler_3.4.2    pillar_1.1.0     
 [4] git2r_0.21.0      plyr_1.8.4        bindr_0.1.1      
 [7] R.methodsS3_1.7.1 R.utils_2.6.0     tools_3.4.2      
[10] digest_0.6.15     evaluate_0.10.1   tibble_1.4.2     
[13] gtable_0.2.0      pkgconfig_2.0.1   rlang_0.2.1      
[16] yaml_2.1.19       stringr_1.3.1     knitr_1.18       
[19] rprojroot_1.3-2   grid_3.4.2        tidyselect_0.2.4 
[22] glue_1.2.0        R6_2.2.2          purrr_0.2.5      
[25] magrittr_1.5      whisker_0.3-2     backports_1.1.2  
[28] scales_0.5.0      htmltools_0.3.6   assertthat_0.2.0 
[31] colorspace_1.3-2  labeling_0.3      stringi_1.2.2    
[34] lazyeval_0.2.1    munsell_0.4.3     R.oo_1.22.0      </code></pre>
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