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<h1 class="title toc-ignore">FLASH2MASH</h1>
<h4 class="author"><em>Briana Mittleman</em></h4>
<h4 class="date"><em>11/6/2018</em></h4>

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<p><strong>Last updated:</strong> 2018-11-06</p>
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Great! You are using Git for version control. Tracking code development and connecting the code version to the results is critical for reproducibility. The version displayed above was the version of the Git repository at the time these results were generated. <br><br> Note that you need to be careful to ensure that all relevant files for the analysis have been committed to Git prior to generating the results (you can use <code>wflow_publish</code> or <code>wflow_git_commit</code>). workflowr only checks the R Markdown file, but you know if there are other scripts or data files that it depends on. Below is the status of the Git repository when the results were generated:
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<a href="https://github.com/brimittleman/threeprimeseq/blob/b5f744f599ad5ec725eb3e31b86e804979f568b2/analysis/flash2mash.Rmd" target="_blank">b5f744f</a>
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Briana Mittleman
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2018-11-06
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<p></details></p>
<hr />
<p>I will use this analysis to implement the flash and mash packages developed by the stephens lab to better understand molecular QTL sharing and to see if adding APA to a model can help with power in protein QTLs.</p>
<p>Steps: 1. FLASH to see tissue patterns (<a href="https://willwerscheid.github.io/MASHvFLASH/MASHvFLASHnn.html" class="uri">https://willwerscheid.github.io/MASHvFLASH/MASHvFLASHnn.html</a> and <a href="https://willwerscheid.github.io/MASHvFLASH/MASHvFLASHnn2.html" class="uri">https://willwerscheid.github.io/MASHvFLASH/MASHvFLASHnn2.html</a>)<br />
2. Conditional analysis with residuals to see if I can call APA qtls on the residuals from an RNA~protein analysis 3. run MASH</p>
<p>Data stucture: I need to have a matrix with all of my QTL results. I want to get a snp-gene by phenotype matrix with the effect sizes and standard errors. First I will do this with the genes we have all data for (unless it is too small). To deal with the APA isoform problem I will use the peak with the most significant peak-snp pair. This should be ok because given the peaks are ratios they are all correlated with eachother.</p>
<pre class="r"><code>library(tidyverse)</code></pre>
<pre><code>── Attaching packages ────────────────────────────────────────────────────────────────────────────── tidyverse 1.2.1 ──</code></pre>
<pre><code>✔ ggplot2 3.0.0     ✔ purrr   0.2.5
✔ tibble  1.4.2     ✔ dplyr   0.7.6
✔ tidyr   0.8.1     ✔ stringr 1.3.1
✔ readr   1.1.1     ✔ forcats 0.3.0</code></pre>
<pre><code>── Conflicts ───────────────────────────────────────────────────────────────────────────────── tidyverse_conflicts() ──
✖ dplyr::filter() masks stats::filter()
✖ dplyr::lag()    masks stats::lag()</code></pre>
<pre class="r"><code>library(workflowr)</code></pre>
<pre><code>This is workflowr version 1.1.1
Run ?workflowr for help getting started</code></pre>
<p>First I can use the permuted results to look at the genes that are tested in all of the phenotypes.</p>
<pre class="r"><code>read_permfile=function(file, mol){
  perm_names=c(&quot;pid&quot; ,&quot;nvar&quot;,&quot;shape1&quot; ,&quot;shape2&quot;, &quot;dummy&quot;,&quot;sid&quot; ,&quot;dist&quot;,&quot;npval&quot;, &quot;slope&quot; , &quot;ppval&quot; ,&quot;bpval&quot;)
  geneNames=read.table(&quot;../data/ensemble_to_genename.txt&quot;, sep=&quot;\t&quot;, header=T,stringsAsFactors = F)
  res=read.table(file, col.names = perm_names, stringsAsFactors = F)
  if (mol == &quot;protein&quot;){
    res_f= res %&gt;% rename(&quot;Gene.stable.ID&quot;=pid)
    res_final= res_f %&gt;% inner_join(geneNames, by=&quot;Gene.stable.ID&quot;) %&gt;% select(c(&quot;Gene.name&quot;))
  }
  else{
    res_final =res %&gt;% separate(pid, into=c(&quot;Gene.stable.ID&quot;, &quot;ver&quot;), sep =&quot;[.]&quot;) %&gt;% inner_join(geneNames, by=&quot;Gene.stable.ID&quot;) %&gt;% select(c(&quot;Gene.name&quot;))
  }
  return(res_final)
}</code></pre>
<pre class="r"><code>prot_res=read_permfile(&quot;../data/other_qtls/fastqtl_qqnorm_prot.fixed.perm.out&quot;, &quot;protein&quot;)
rna_res=read_permfile(&quot;../data/other_qtls/fastqtl_qqnorm_RNAseq_phase2.fixed.perm.out&quot;, &quot;RNA&quot;)
rnaG_res=read_permfile(&quot;../data/other_qtls/fastqtl_qqnorm_RNAseqGeuvadis.fixed.perm.out&quot;, &quot;RNAG&quot;)
su30_res=read_permfile(&quot;../data/other_qtls/fastqtl_qqnorm_4su30.fixed.perm.out&quot;, &quot;su30&quot;)
su60_res=read_permfile(&quot;../data/other_qtls/fastqtl_qqnorm_4su60.fixed.perm.out&quot;, &quot;su60&quot;)
ribo_res=read_permfile(&quot;../data/other_qtls/fastqtl_qqnorm_ribo_phase2.fixed.perm.out&quot;, &quot;ribo&quot;)</code></pre>
<p>Now I need to look at the apa file genes.</p>
<pre class="r"><code>NuclearAPA=read.table(&quot;../data/perm_QTL_trans/filtered_APApeaks_merged_allchrom_refseqGenes_pheno_Nuclear_transcript_permResBH.txt&quot;, stringsAsFactors = F, header=T)  %&gt;%  separate(pid, sep = &quot;:&quot;, into=c(&quot;chr&quot;, &quot;start&quot;, &quot;end&quot;, &quot;id&quot;)) %&gt;% separate(id, sep = &quot;_&quot;, into=c(&quot;gene&quot;, &quot;strand&quot;, &quot;peak&quot;)) %&gt;%  rename(&quot;Gene.name&quot;=gene) %&gt;% select(Gene.name)%&gt;% distinct()

totalAPA=read.table(&quot;../data/perm_QTL_trans/filtered_APApeaks_merged_allchrom_refseqGenes_pheno_Total_transcript_permResBH.txt&quot;, stringsAsFactors = F, header=T)  %&gt;%  separate(pid, sep = &quot;:&quot;, into=c(&quot;chr&quot;, &quot;start&quot;, &quot;end&quot;, &quot;id&quot;)) %&gt;% separate(id, sep = &quot;_&quot;, into=c(&quot;gene&quot;, &quot;strand&quot;, &quot;peak&quot;)) %&gt;% rename(&quot;Gene.name&quot;=gene) %&gt;% select(Gene.name) %&gt;% distinct()</code></pre>
<p>Look hoqw many genes are in all sets:</p>
<pre class="r"><code>allgenes= NuclearAPA %&gt;% inner_join(totalAPA,by=&quot;Gene.name&quot;) %&gt;% inner_join(totalAPA,by=&quot;Gene.name&quot;) %&gt;% inner_join(su30_res,by=&quot;Gene.name&quot;) %&gt;% inner_join(su60_res,by=&quot;Gene.name&quot;) %&gt;% inner_join(rna_res,by=&quot;Gene.name&quot;) %&gt;% inner_join(rnaG_res,by=&quot;Gene.name&quot;)%&gt;% inner_join(ribo_res,by=&quot;Gene.name&quot;)%&gt;% inner_join(prot_res,by=&quot;Gene.name&quot;)
print(nrow(allgenes))</code></pre>
<pre><code>[1] 904</code></pre>
<pre class="r"><code>allgenes_minusprot= NuclearAPA %&gt;% inner_join(totalAPA,by=&quot;Gene.name&quot;) %&gt;% inner_join(totalAPA,by=&quot;Gene.name&quot;) %&gt;% inner_join(su30_res,by=&quot;Gene.name&quot;) %&gt;% inner_join(su60_res,by=&quot;Gene.name&quot;) %&gt;% inner_join(rna_res,by=&quot;Gene.name&quot;) %&gt;% inner_join(rnaG_res,by=&quot;Gene.name&quot;)%&gt;% inner_join(ribo_res,by=&quot;Gene.name&quot;)
print(nrow(allgenes_minusprot))</code></pre>
<pre><code>[1] 2195</code></pre>
<pre class="r"><code>allgenes_minusribo= NuclearAPA %&gt;% inner_join(totalAPA,by=&quot;Gene.name&quot;) %&gt;% inner_join(totalAPA,by=&quot;Gene.name&quot;) %&gt;% inner_join(su30_res,by=&quot;Gene.name&quot;) %&gt;% inner_join(su60_res,by=&quot;Gene.name&quot;) %&gt;% inner_join(rna_res,by=&quot;Gene.name&quot;) %&gt;% inner_join(rnaG_res,by=&quot;Gene.name&quot;)%&gt;% inner_join(prot_res,by=&quot;Gene.name&quot;)
print(nrow(allgenes_minusribo))</code></pre>
<pre><code>[1] 904</code></pre>
<pre class="r"><code>genes_ApaRnaProt= NuclearAPA %&gt;% inner_join(totalAPA,by=&quot;Gene.name&quot;) %&gt;%inner_join(rna_res,by=&quot;Gene.name&quot;) %&gt;%inner_join(prot_res,by=&quot;Gene.name&quot;)
print(nrow(genes_ApaRnaProt))</code></pre>
<pre><code>[1] 904</code></pre>
<pre class="r"><code>genes_RNAProt= rna_res%&gt;%inner_join(prot_res,by=&quot;Gene.name&quot;)
print(nrow(genes_RNAProt))</code></pre>
<pre><code>[1] 4131</code></pre>
<p>Only have 904 genes that are tested in both APA and protein data.</p>
<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     

other attached packages:
 [1] workflowr_1.1.1 forcats_0.3.0   stringr_1.3.1   dplyr_0.7.6    
 [5] purrr_0.2.5     readr_1.1.1     tidyr_0.8.1     tibble_1.4.2   
 [9] ggplot2_3.0.0   tidyverse_1.2.1

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.19      cellranger_1.1.0  plyr_1.8.4       
 [4] compiler_3.5.1    pillar_1.3.0      git2r_0.23.0     
 [7] bindr_0.1.1       R.methodsS3_1.7.1 R.utils_2.7.0    
[10] tools_3.5.1       digest_0.6.17     lubridate_1.7.4  
[13] jsonlite_1.5      evaluate_0.11     nlme_3.1-137     
[16] gtable_0.2.0      lattice_0.20-35   pkgconfig_2.0.2  
[19] rlang_0.2.2       cli_1.0.1         rstudioapi_0.8   
[22] yaml_2.2.0        haven_1.1.2       bindrcpp_0.2.2   
[25] withr_2.1.2       xml2_1.2.0        httr_1.3.1       
[28] knitr_1.20        hms_0.4.2         rprojroot_1.3-2  
[31] grid_3.5.1        tidyselect_0.2.4  glue_1.3.0       
[34] R6_2.3.0          readxl_1.1.0      rmarkdown_1.10   
[37] modelr_0.1.2      magrittr_1.5      whisker_0.3-2    
[40] backports_1.1.2   scales_1.0.0      htmltools_0.3.6  
[43] rvest_0.3.2       assertthat_0.2.0  colorspace_1.3-2 
[46] stringi_1.2.4     lazyeval_0.2.1    munsell_0.5.0    
[49] broom_0.5.0       crayon_1.3.4      R.oo_1.22.0      </code></pre>
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