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} </style> <div class="fluid-row" id="header"> <h1 class="title toc-ignore">Test SMASH</h1> <h4 class="author"><em>Briana Mittleman</em></h4> <h4 class="date"><em>7/16/2018</em></h4> </div> <p><strong>Last updated:</strong> 2018-07-19</p> <strong>workflowr checks:</strong> <small>(Click a bullet for more information)</small> <ul> <li> <p><details> <summary> <strong style="color:blue;">✔</strong> <strong>R Markdown file:</strong> up-to-date </summary></p> <p>Great! 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Setting a seed ensures that any results that rely on randomness, e.g. subsampling or permutations, are reproducible.</p> </details> </li> <li> <p><details> <summary> <strong style="color:blue;">✔</strong> <strong>Session information:</strong> recorded </summary></p> <p>Great job! Recording the operating system, R version, and package versions is critical for reproducibility.</p> </details> </li> <li> <p><details> <summary> <strong style="color:blue;">✔</strong> <strong>Repository version:</strong> <a href="https://github.com/brimittleman/threeprimeseq/tree/8398e0e78fd6ed476cfd5361295c1497c9841f60" target="_blank">8398e0e</a> </summary></p> 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: <pre><code> Ignored files: Ignored: .DS_Store Ignored: .Rhistory Ignored: .Rproj.user/ Ignored: output/.DS_Store Untracked files: Untracked: data/18486.genecov.txt Untracked: data/APApeaksYL.total.inbrain.bed Untracked: data/YL-SP-18486-T_S9_R1_001-genecov.txt Untracked: data/bedgraph_peaks/ Untracked: data/bin200.5.T.nuccov.bed Untracked: data/bin200.Anuccov.bed Untracked: data/bin200.nuccov.bed Untracked: data/gene_cov/ Untracked: data/leafcutter/ Untracked: data/nuc6up/ Untracked: data/reads_mapped_three_prime_seq.csv Untracked: data/smash.cov.results.bed Untracked: data/smash.cov.results.csv Untracked: data/smash.cov.results.txt Untracked: data/smash_testregion/ Untracked: data/ssFC200.cov.bed Untracked: output/picard/ Untracked: output/plots/ Untracked: output/qual.fig2.pdf Unstaged changes: Modified: analysis/dif.iso.usage.leafcutter.Rmd Modified: analysis/explore.filters.Rmd Modified: analysis/test.max2.Rmd Modified: code/Snakefile </code></pre> Note that any generated files, e.g. HTML, png, CSS, etc., are not included in this status report because it is ok for generated content to have uncommitted changes. </details> </li> </ul> <details> <summary> <small><strong>Expand here to see past versions:</strong></small> </summary> <ul> <table style="border-collapse:separate; border-spacing:5px;"> <thead> <tr> <th style="text-align:left;"> File </th> <th style="text-align:left;"> Version </th> <th style="text-align:left;"> Author </th> <th style="text-align:left;"> Date </th> <th style="text-align:left;"> Message </th> </tr> </thead> <tbody> <tr> <td style="text-align:left;"> Rmd </td> <td style="text-align:left;"> <a href="https://github.com/brimittleman/threeprimeseq/blob/8398e0e78fd6ed476cfd5361295c1497c9841f60/analysis/test.smash.Rmd" target="_blank">8398e0e</a> </td> <td style="text-align:left;"> Briana Mittleman </td> <td style="text-align:left;"> 2018-07-19 </td> <td style="text-align:left;"> run on all ind </td> </tr> <tr> <td style="text-align:left;"> html </td> <td style="text-align:left;"> <a href="https://cdn.rawgit.com/brimittleman/threeprimeseq/652b7e9a399ef80fef98e1a7943cd2224b154c9a/docs/test.smash.html" target="_blank">652b7e9</a> </td> <td style="text-align:left;"> Briana Mittleman </td> <td style="text-align:left;"> 2018-07-19 </td> <td style="text-align:left;"> Build site. </td> </tr> <tr> <td style="text-align:left;"> Rmd </td> <td style="text-align:left;"> <a href="https://github.com/brimittleman/threeprimeseq/blob/31482e2756b96a67021ff4f25923469e45a99453/analysis/test.smash.Rmd" target="_blank">31482e2</a> </td> <td style="text-align:left;"> Briana Mittleman </td> <td style="text-align:left;"> 2018-07-19 </td> <td style="text-align:left;"> gapdh </td> </tr> <tr> <td style="text-align:left;"> html </td> <td style="text-align:left;"> <a href="https://cdn.rawgit.com/brimittleman/threeprimeseq/319322373c1d7d83d53b6eb868a5fefae3dd682d/docs/test.smash.html" target="_blank">3193223</a> </td> <td style="text-align:left;"> Briana Mittleman </td> <td style="text-align:left;"> 2018-07-18 </td> <td style="text-align:left;"> Build site. </td> </tr> <tr> <td style="text-align:left;"> Rmd </td> <td style="text-align:left;"> <a href="https://github.com/brimittleman/threeprimeseq/blob/9d320762cc20d555c01ef24c55f9b9c5253631f7/analysis/test.smash.Rmd" target="_blank">9d32076</a> </td> <td style="text-align:left;"> Briana Mittleman </td> <td style="text-align:left;"> 2018-07-18 </td> <td style="text-align:left;"> add actb example </td> </tr> <tr> <td style="text-align:left;"> html </td> <td style="text-align:left;"> <a href="https://cdn.rawgit.com/brimittleman/threeprimeseq/0464829eb7efe6e59a1e4c9b119aacf011b4bdaa/docs/test.smash.html" target="_blank">0464829</a> </td> <td style="text-align:left;"> Briana Mittleman </td> <td style="text-align:left;"> 2018-07-17 </td> <td style="text-align:left;"> Build site. </td> </tr> <tr> <td style="text-align:left;"> Rmd </td> <td style="text-align:left;"> <a href="https://github.com/brimittleman/threeprimeseq/blob/cc5cc50c1522e65db9c5347be32b84b8a3cc8701/analysis/test.smash.Rmd" target="_blank">cc5cc50</a> </td> <td style="text-align:left;"> Briana Mittleman </td> <td style="text-align:left;"> 2018-07-17 </td> <td style="text-align:left;"> test region smash results </td> </tr> <tr> <td style="text-align:left;"> html </td> <td style="text-align:left;"> <a href="https://cdn.rawgit.com/brimittleman/threeprimeseq/d61f59030ac60a83efbe121b621608644b6a3203/docs/test.smash.html" target="_blank">d61f590</a> </td> <td style="text-align:left;"> Briana Mittleman </td> <td style="text-align:left;"> 2018-07-17 </td> <td style="text-align:left;"> Build site. </td> </tr> <tr> <td style="text-align:left;"> Rmd </td> <td style="text-align:left;"> <a href="https://github.com/brimittleman/threeprimeseq/blob/89ebcac67144a2affcfc48336fd37621f7c74833/analysis/test.smash.Rmd" target="_blank">89ebcac</a> </td> <td style="text-align:left;"> Briana Mittleman </td> <td style="text-align:left;"> 2018-07-17 </td> <td style="text-align:left;"> add smash test </td> </tr> </tbody> </table> </ul> <p></details></p> <hr /> <p>In this analysis I will use the tutorial I did for the SMASH package on chip seq data to test it on the three prime seq data. In order to complete this I need to make a matrix with genome location counts for where reads start for positions 880001:1011072 on chr1, I am using this region because I already know it fits the <span class="math inline">\(2^{x}\)</span> criterion. I need the matrix to be individual by basepair. I can use genome cov in all of the total fractions then merge the results together to make a matrix.</p> <div id="create-coverage-files" class="section level2"> <h2>Create Coverage files</h2> <pre class="bash"><code>#!/bin/bash #SBATCH --job-name=5gencov #SBATCH --account=pi-yangili1 #SBATCH --time=24:00:00 #SBATCH --output=5gencov.out #SBATCH --error=5gencov.err #SBATCH --partition=broadwl #SBATCH --mem=40G #SBATCH --mail-type=END module load Anaconda3 source activate three-prime-env #imput sorted bam file bam=$1 describer=$(echo ${bam} | sed -e 's/.*\YL-SP-//' | sed -e "s/-sort.bam$//") bedtools genomecov-ibam $1 -d -5 > /project2/gilad/briana/threeprimeseq/data/test.smash/gencov5prime.${describer}.bed</code></pre> <p>run on /project2/gilad/briana/threeprimeseq/data/sort/YL-SP-18486-N_S10_R1_001-sort.bam</p> <p>wrap this function:</p> <pre class="bash"><code>#!/bin/bash #SBATCH --job-name=w_5gencov #SBATCH --account=pi-yangili1 #SBATCH --time=24:00:00 #SBATCH --output=w_5gencov.out #SBATCH --error=w_5gencov.err #SBATCH --partition=broadwl #SBATCH --mem=16G #SBATCH --mail-type=END module load Anaconda3 source activate three-prime-env for i in $(ls /project2/gilad/briana/threeprimeseq/data/sort/*.bam); do sbatch 5primegencov.sh $i done</code></pre> </div> <div id="test-example-region" class="section level2"> <h2>Test example region</h2> <p>First I will get ch1 880001:1011072 for each individual.</p> <pre class="bash"><code>#!/bin/bash #SBATCH --job-name=test.reg #SBATCH --account=pi-yangili1 #SBATCH --time=24:00:00 #SBATCH --output=test.reg.out #SBATCH --error=test.reg.err #SBATCH --partition=broadwl #SBATCH --mem=20G #SBATCH --mail-type=END awk '$1 == 1 && $2 >= 880001 && $2 <= 1011072 {print}' /project2/gilad/briana/threeprimeseq/data/test.smash/gencov5prime.18486-T_S9_R1_001.bed > /project2/gilad/briana/threeprimeseq/data/test.region/gencov5prime.18486-T_S9_R1_001.testregion.bed awk '$1 == 1 && $2 >= 880001 && $2 <= 1011072 {print}' /project2/gilad/briana/threeprimeseq/data/test.smash/gencov5prime.18497-T_S11_R1_001.bed > /project2/gilad/briana/threeprimeseq/data/test.region/gencov5prime.18497-T_S11_R1_001.testregion.bed awk '$1 == 1 && $2 >= 880001 &5& $2 <= 1011072 {print}' /project2/gilad/briana/threeprimeseq/data/test.smash/gencov5prime.18500-T_S19_R1_001.bed > /project2/gilad/briana/threeprimeseq/data/test.region/gencov5prime.18500-T_S19_R1_001.testregion.bed awk '$1 == 1 && $2 >= 880001 && $2 <= 1011072 {print}' /project2/gilad/briana/threeprimeseq/data/test.smash/gencov5prime.18505-T_S1_R1_001.bed > /project2/gilad/briana/threeprimeseq/data/test.region/gencov5prime.18505-T_S1_R1_001.testregion.bed awk '$1 == 1 && $2 >= 880001 && $2 <= 1011072 {print}' gencov5prime.18508-T_S5_R1_001.bed > /project2/gilad/briana/threeprimeseq/data/test.region/gencov5prime.18508-T_S5_R1_001.testregion.bed awk '$1 == 1 && $2 >= 880001 && $2 <= 1011072 {print}'/project2/gilad/briana/threeprimeseq/data/test.smash/gencov5prime.18853-T_S31_R1_001.bed > /project2/gilad/briana/threeprimeseq/data/test.region/gencov5prime.18853-T_S31_R1_001.testregion.bed awk '$1 == 1 && $2 >= 880001 && $2 <= 1011072 {print}' /project2/gilad/briana/threeprimeseq/data/test.smash/gencov5prime.18870-T_S23_R1_001.bed > /project2/gilad/briana/threeprimeseq/data/test.region/gencov5prime.18870-T_S23_R1_001.testregion.bed awk '$1 == 1 && $2 >= 880001 && $2 <= 1011072 {print}' /project2/gilad/briana/threeprimeseq/data/test.smash/gencov5prime.19128-T_S29_R1_001.bed > /project2/gilad/briana/threeprimeseq/data/test.region/gencov5prime.19128-T_S29_R1_001.testregion.bed awk '$1 == 1 && $2 >= 880001 && $2 <= 1011072 {print}' /project2/gilad/briana/threeprimeseq/data/test.smash/gencov5prime.19141-T_S17_R1_001.bed > /project2/gilad/briana/threeprimeseq/data/test.region/gencov5prime.19141-T_S17_R1_001.testregion.bed awk '$1 == 1 && $2 >= 880001 && $2 <= 1011072 {print}' /project2/gilad/briana/threeprimeseq/data/test.smash/gencov5prime.19193-T_S21_R1_001.bed > /project2/gilad/briana/threeprimeseq/data/test.region/gencov5prime.19193-T_S21_R1_001.testregion.bed awk '$1 == 1 && $2 >= 880001 && $2 <= 1011072 {print}' /project2/gilad/briana/threeprimeseq/data/test.smash/gencov5prime.19209-T_S15_R1_001.bed > /project2/gilad/briana/threeprimeseq/data/test.region/gencov5prime.19209-T_S15_R1_001.testregion.bed awk '$1 == 1 && $2 >= 880001 && $2 <= 1011072 {print}' /project2/gilad/briana/threeprimeseq/data/test.smash/gencov5prime.19233-T_S7_R1_001.bed > /project2/gilad/briana/threeprimeseq/data/test.region/gencov5prime.19223-T_S7_R1_001.testregion.bed awk '$1 == 1 && $2 >= 880001 && $2 <= 1011072 {print}' /project2/gilad/briana/threeprimeseq/data/test.smash/gencov5prime.19225-T_S27_R1_001.bed > /project2/gilad/briana/threeprimeseq/data/test.region/gencov5prime.19225-T_S27_R1_001.testregion.bed awk '$1 == 1 && $2 >= 880001 && $2 <= 1011072 {print}' /project2/gilad/briana/threeprimeseq/data/test.smash/gencov5prime.19238-T_S3_R1_001.bed > /project2/gilad/briana/threeprimeseq/data/test.region/gencov5prime.19238-T_S3_R1_001.testregion.bed awk '$1 == 1 && $2 >= 880001 && $2 <= 1011072 {print}' /project2/gilad/briana/threeprimeseq/data/test.smash/gencov5prime.19239-T_S13_R1_001.bed > /project2/gilad/briana/threeprimeseq/data/test.region/gencov5prime.19239-T_S13_R1_001.testregion.bed awk '$1 == 1 && $2 >= 880001 && $2 <= 1011072 {print}' /project2/gilad/briana/threeprimeseq/data/test.smash/gencov5prime.19257-T_S25_R1_001.bed > /project2/gilad/briana/threeprimeseq/data/test.region/gencov5prime.19257-T_S25_R1_001.testregion.bed </code></pre> <p>3 didnt work. Try these again.</p> <pre class="bash"><code> #!/bin/bash #SBATCH --job-name=test.reg2 #SBATCH --account=pi-yangili1 #SBATCH --time=24:00:00 #SBATCH --output=test.reg2.out #SBATCH --error=test.reg2.err #SBATCH --partition=broadwl #SBATCH --mem=20G #SBATCH --mail-type=END awk '$1 == 1 && $2 >= 880001 && $2 <= 1011072 {print}' /project2/gilad/briana/threeprimeseq/data/test.smash/gencov5prime.18508-T_S5_R1_001.bed > /project2/gilad/briana/threeprimeseq/data/test.region/gencov5prime.18508-T_S5_R1_001.testregion.bed awk '$1 == 1 && $2 >= 880001 && $2 <= 1011072 {print}' /project2/gilad/briana/threeprimeseq/data/test.smash/gencov5prime.18853-T_S31_R1_001.bed > /project2/gilad/briana/threeprimeseq/data/test.region/gencov5prime.18853-T_S31_R1_001.testregion.bed awk '$1 == 1 && $2 >= 880001 && $2 <= 1011072 {print}' /project2/gilad/briana/threeprimeseq/data/test.smash/gencov5prime.18500-T_S19_R1_001.bed > /project2/gilad/briana/threeprimeseq/data/test.region/gencov5prime.18500-T_S19_R1_001.testregion.bed </code></pre> <p>Now I will pull in these regions and merge them to make a matrix I can put into smashr.</p> <pre class="r"><code>test_18468=read.table("../data/smash_testregion/gencov5prime.18486-T_S9_R1_001.testregion.bed", col.names=c("chr", "base", "T18486")) test_18497=read.table("../data/smash_testregion/gencov5prime.18497-T_S11_R1_001.testregion.bed", col.names=c("chr", "base", "T18497")) test_18500=read.table("../data/smash_testregion/gencov5prime.18500-T_S19_R1_001.testregion.bed", col.names=c("chr", "base", "T18500")) test_18505=read.table("../data/smash_testregion/gencov5prime.18505-T_S1_R1_001.testregion.bed", col.names=c("chr", "base", "T18505")) test_18508=read.table("../data/smash_testregion/gencov5prime.18508-T_S5_R1_001.testregion.bed", col.names=c("chr", "base", "T18508")) test_18853=read.table("../data/smash_testregion/gencov5prime.18853-T_S31_R1_001.testregion.bed", col.names=c("chr", "base", "T18853")) test_18870=read.table("../data/smash_testregion/gencov5prime.18870-T_S23_R1_001.testregion.bed", col.names=c("chr", "base", "T18870")) test_19128=read.table("../data/smash_testregion/gencov5prime.19128-T_S29_R1_001.testregion.bed", col.names=c("chr", "base", "T19128")) test_19239=read.table("../data/smash_testregion/gencov5prime.19239-T_S13_R1_001.testregion.bed", col.names=c("chr", "base", "T19239")) test_19257=read.table("../data/smash_testregion/gencov5prime.19257-T_S25_R1_001.testregion.bed", col.names=c("chr", "base", "T19257")) test_19141=read.table("../data/smash_testregion/gencov5prime.19141-T_S17_R1_001.testregion.bed", col.names=c("chr", "base", "T19141")) test_19193=read.table("../data/smash_testregion/gencov5prime.19193-T_S21_R1_001.testregion.bed", col.names=c("chr", "base", "T19193")) test_19209=read.table("../data/smash_testregion/gencov5prime.19209-T_S15_R1_001.testregion.bed", col.names=c("chr", "base", "T19209")) test_19223=read.table("../data/smash_testregion/gencov5prime.19223-T_S7_R1_001.testregion.bed", col.names=c("chr", "base", "T19223")) test_19225=read.table("../data/smash_testregion/gencov5prime.19225-T_S27_R1_001.testregion.bed", col.names=c("chr", "base", "T19225")) test_19238=read.table("../data/smash_testregion/gencov5prime.19238-T_S3_R1_001.testregion.bed", col.names=c("chr", "base", "T19238"))</code></pre> <p>Load Packages:</p> <pre class="r"><code>library(devtools)</code></pre> <pre><code>Warning: package 'devtools' was built under R version 3.4.4</code></pre> <pre class="r"><code>library(scales) library(smashr) library(tidyr) 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(dplyr)</code></pre> <pre><code>Warning: package 'dplyr' was built under R version 3.4.4</code></pre> <pre><code> Attaching package: 'dplyr'</code></pre> <pre><code>The following objects are masked from 'package:stats': filter, lag</code></pre> <pre><code>The following objects are masked from 'package:base': intersect, setdiff, setequal, union</code></pre> <p>Bind all of the count</p> <pre class="r"><code>test_matrix=cbind(test_18468$T18486, test_18497$T18497, test_18500$T18500, test_18505$T18505, test_18508$T18508, test_18853$T18853, test_18870$T18870, test_19128$T19128, test_19141$T19141, test_19193$T19193, test_19209$T19209, test_19223$T19223, test_19225$T19225, test_19238$T19238, test_19239$T19239, test_19257$T19257) %>% t</code></pre> <p>Run smash:</p> <pre class="r"><code>res = smash.poiss(test_matrix[1,]+test_matrix[2,],post.var=TRUE)</code></pre> <pre><code>Due to absence of package REBayes, switching to EM algorithm Due to absence of package REBayes, switching to EM algorithm Due to absence of package REBayes, switching to EM algorithm Due to absence of package REBayes, switching to EM algorithm Due to absence of package REBayes, switching to EM algorithm Due to absence of package REBayes, switching to EM algorithm Due to absence of package REBayes, switching to EM algorithm Due to absence of package REBayes, switching to EM algorithm Due to absence of package REBayes, switching to EM algorithm Due to absence of package REBayes, switching to EM algorithm Due to absence of package REBayes, switching to EM algorithm Due to absence of package REBayes, switching to EM algorithm</code></pre> <pre><code>Squarem-1 Objective fn: 316440 Objective fn: 75069.3 Extrapolation: 0 Steplength: 1 Objective fn: 20919.7 Extrapolation: 1 Steplength: 1.7761 Objective fn: 17547 Extrapolation: 1 Steplength: 4 Objective fn: 17138.8 Extrapolation: 1 Steplength: 4.55255 Objective fn: 16836.6 Extrapolation: 1 Steplength: 1.86253 Objective fn: 16818.8 Extrapolation: 1 Steplength: 6.42316 Objective fn: 16816 Extrapolation: 1 Steplength: 1.66778 Objective fn: 16815.9 Extrapolation: 1 Steplength: 7.08232</code></pre> <pre><code>Due to absence of package REBayes, switching to EM algorithm</code></pre> <pre><code>Squarem-1 Objective fn: 547800 Objective fn: 101309 Extrapolation: 0 Steplength: 1 Objective fn: 37390.2 Extrapolation: 1 Steplength: 1.89191 Objective fn: 32343.6 Extrapolation: 1 Steplength: 4 Objective fn: 31416.8 Extrapolation: 1 Steplength: 5.23485 Objective fn: 31019 Extrapolation: 1 Steplength: 2.24046 Objective fn: 31004.3 Extrapolation: 1 Steplength: 5.95071 Objective fn: 31003.4 Extrapolation: 1 Steplength: 2.25357 Objective fn: 31003.3 Extrapolation: 1 Steplength: 6.79538</code></pre> <pre><code>Due to absence of package REBayes, switching to EM algorithm</code></pre> <pre><code>Squarem-1 Objective fn: 882921 Objective fn: 118772 Extrapolation: 0 Steplength: 1 Objective fn: 49764.5 Extrapolation: 1 Steplength: 1.87244 Objective fn: 44341.9 Extrapolation: 1 Steplength: 4 Objective fn: 43183.7 Extrapolation: 1 Steplength: 4.56042 Objective fn: 41597.4 Extrapolation: 1 Steplength: 1.93991 Objective fn: 41582.5 Extrapolation: 1 Steplength: 7.15247 Objective fn: 41416.1 Extrapolation: 1 Steplength: 1.69043 Objective fn: 41408.8 Extrapolation: 1 Steplength: 9.74108 Objective fn: 41406.9 Extrapolation: 1 Steplength: 1.59935 Objective fn: 41406.9 Extrapolation: 1 Steplength: 5.74521 Objective fn: 41406.8 Extrapolation: 1 Steplength: 3.48951</code></pre> <pre><code>Due to absence of package REBayes, switching to EM algorithm</code></pre> <pre><code>Squarem-1 Objective fn: 1.2791e+06 Objective fn: 88217.7 Extrapolation: 0 Steplength: 1 Objective fn: 48098 Extrapolation: 1 Steplength: 3.21173 Objective fn: 41534.8 Extrapolation: 1 Steplength: 3.31029 Objective fn: 39112.5 Extrapolation: 1 Steplength: 1.9387 Objective fn: 38929.7 Extrapolation: 1 Steplength: 4 Objective fn: 38852.8 Extrapolation: 1 Steplength: 1.89245 Objective fn: 38845.6 Extrapolation: 1 Steplength: 5.02972 Objective fn: 38844.1 Extrapolation: 1 Steplength: 1.53262 Objective fn: 38843.9 Extrapolation: 1 Steplength: 6.32374</code></pre> <pre><code>Due to absence of package REBayes, switching to EM algorithm</code></pre> <pre><code>Squarem-1 Objective fn: 1.19992e+06 Objective fn: 127113 Extrapolation: 0 Steplength: 1 Objective fn: 103768 Extrapolation: 1 Steplength: 2.87597 Objective fn: 100999 Extrapolation: 1 Steplength: 4 Objective fn: 99983.8 Extrapolation: 1 Steplength: 3.04432 Objective fn: 99154 Extrapolation: 1 Steplength: 4.6448 Objective fn: 98661.4 Extrapolation: 1 Steplength: 2.95052 Objective fn: 98391.1 Extrapolation: 1 Steplength: 5.09439 Objective fn: 98302.4 Extrapolation: 1 Steplength: 2.05767 Objective fn: 98288.2 Extrapolation: 1 Steplength: 13.5878 Objective fn: 98224.6 Extrapolation: 1 Steplength: 1.53983 Objective fn: 98212.4 Extrapolation: 1 Steplength: 16 Objective fn: 98207 Extrapolation: 1 Steplength: 2.54441 Objective fn: 98203.1 Extrapolation: 1 Steplength: 8.20699 Objective fn: 98202 Extrapolation: 1 Steplength: 2.00162 Objective fn: 98199.8 Extrapolation: 1 Steplength: 16.5155 Objective fn: 98198.5 Extrapolation: 1 Steplength: 1.62338 Objective fn: 98199 Extrapolation: 1 Steplength: 44.8518 Objective fn: 98195.9 Extrapolation: 1 Steplength: 1.4749 Objective fn: 98195.6 Extrapolation: 0 Steplength: 1 Objective fn: 98195.4 Extrapolation: 0 Steplength: 1 Objective fn: 98195.2 Extrapolation: 0 Steplength: 1 Objective fn: 98195.1 Extrapolation: 0 Steplength: 1 Objective fn: 98194.8 Extrapolation: 1 Steplength: 16 Objective fn: 98194.6 Extrapolation: 0 Steplength: 1 Objective fn: 98194.5 Extrapolation: 0 Steplength: 1 Objective fn: 98194.4 Extrapolation: 0 Steplength: 1 Objective fn: 98194.2 Extrapolation: 1 Steplength: 16 Objective fn: 98194 Extrapolation: 0 Steplength: 1 Objective fn: 98193.9 Extrapolation: 0 Steplength: 1 Objective fn: 98193.7 Extrapolation: 1 Steplength: 16 Objective fn: 98193.6 Extrapolation: 0 Steplength: 1 Objective fn: 98193.5 Extrapolation: 0 Steplength: 1 Objective fn: 98193.4 Extrapolation: 0 Steplength: 1 Objective fn: 98193 Extrapolation: 1 Steplength: 16 Objective fn: 98192.9 Extrapolation: 0 Steplength: 1 Objective fn: 98192.8 Extrapolation: 0 Steplength: 1 Objective fn: 98192.7 Extrapolation: 0 Steplength: 1 Objective fn: 98192.1 Extrapolation: 1 Steplength: 16 Objective fn: 98192 Extrapolation: 0 Steplength: 1 Objective fn: 98191.9 Extrapolation: 0 Steplength: 1 Objective fn: 98190.9 Extrapolation: 1 Steplength: 16 Objective fn: 98190.8 Extrapolation: 0 Steplength: 1 Objective fn: 98190.6 Extrapolation: 0 Steplength: 1 Objective fn: 98189.2 Extrapolation: 1 Steplength: 16 Objective fn: 98189 Extrapolation: 0 Steplength: 1 Objective fn: 98186.8 Extrapolation: 1 Steplength: 16 Objective fn: 98186.6 Extrapolation: 0 Steplength: 1 Objective fn: 98183.6 Extrapolation: 1 Steplength: 16 Objective fn: 98183.3 Extrapolation: 0 Steplength: 1 Objective fn: 98179.6 Extrapolation: 1 Steplength: 16 Objective fn: 98179.1 Extrapolation: 0 Steplength: 1 Objective fn: 98175 Extrapolation: 1 Steplength: 16 Objective fn: 98174.4 Extrapolation: 0 Steplength: 1 Objective fn: 98171 Extrapolation: 1 Steplength: 16 Objective fn: 98170.2 Extrapolation: 0 Steplength: 1 Objective fn: 98169.6 Extrapolation: 0 Steplength: 1 Objective fn: 98167.5 Extrapolation: 1 Steplength: 16 Objective fn: 98166.5 Extrapolation: 0 Steplength: 1 Objective fn: 98165.9 Extrapolation: 0 Steplength: 1 Objective fn: 98165.4 Extrapolation: 0 Steplength: 1 Objective fn: 98164.7 Extrapolation: 1 Steplength: 16 Objective fn: 98163.9 Extrapolation: 0 Steplength: 1 Objective fn: 98163.3 Extrapolation: 0 Steplength: 1 Objective fn: 98163 Extrapolation: 0 Steplength: 1 Objective fn: 98162.7 Extrapolation: 0 Steplength: 1 Objective fn: 98162.6 Extrapolation: 1 Steplength: 16 Objective fn: 98162.1 Extrapolation: 0 Steplength: 1 Objective fn: 98161.8 Extrapolation: 0 Steplength: 1 Objective fn: 98161.6 Extrapolation: 0 Steplength: 1 Objective fn: 98161.5 Extrapolation: 0 Steplength: 1 Objective fn: 98161.4 Extrapolation: 0 Steplength: 1 Objective fn: 98161.3 Extrapolation: 0 Steplength: 1 Objective fn: 98161.2 Extrapolation: 1 Steplength: 16 Objective fn: 98161.1 Extrapolation: 0 Steplength: 1 Objective fn: 98161 Extrapolation: 0 Steplength: 1 Objective fn: 98160.9 Extrapolation: 0 Steplength: 1 Objective fn: 98160.9 Extrapolation: 0 Steplength: 1 Objective fn: 98160.9 Extrapolation: 0 Steplength: 1 Objective fn: 98160.9 Extrapolation: 1 Steplength: 16 Objective fn: 98160.8 Extrapolation: 0 Steplength: 1 Objective fn: 98160.8 Extrapolation: 0 Steplength: 1 Objective fn: 98160.8 Extrapolation: 0 Steplength: 1 Objective fn: 98160.8 Extrapolation: 0 Steplength: 1 Objective fn: 98160.7 Extrapolation: 0 Steplength: 1 Objective fn: 98160.7 Extrapolation: 1 Steplength: 16 Objective fn: 98160.7 Extrapolation: 0 Steplength: 1 Objective fn: 98160.7 Extrapolation: 0 Steplength: 1 Objective fn: 98160.7 Extrapolation: 0 Steplength: 1 Objective fn: 98160.7 Extrapolation: 1 Steplength: 16 Objective fn: 98160.7 Extrapolation: 0 Steplength: 1 Objective fn: 98160.7 Extrapolation: 0 Steplength: 1 Objective fn: 98160.7 Extrapolation: 0 Steplength: 1 Objective fn: 98160.7 Extrapolation: 1 Steplength: 16 Objective fn: 98160.7 Extrapolation: 0 Steplength: 1 Objective fn: 98160.7 Extrapolation: 0 Steplength: 1 Objective fn: 98160.7 Extrapolation: 0 Steplength: 1 Objective fn: 98160.7 Extrapolation: 1 Steplength: 16 Objective fn: 98161.6 Extrapolation: 1 Steplength: 25.5964 Objective fn: 98160.7 Extrapolation: 1 Steplength: 4.9659 Objective fn: 98160.7 Extrapolation: 0 Steplength: 1 Objective fn: 98160.7 Extrapolation: 1 Steplength: 16 Objective fn: 98160.7 Extrapolation: 0 Steplength: 1 Objective fn: 98160.6 Extrapolation: 0 Steplength: 1 Objective fn: 98160.6 Extrapolation: 0 Steplength: 1 Objective fn: 98160.7 Extrapolation: 1 Steplength: 16 Objective fn: 98161.4 Extrapolation: 1 Steplength: 28.4418 Objective fn: 98160.6 Extrapolation: 1 Steplength: 4.88053 Objective fn: 98161.5 Extrapolation: 1 Steplength: 64 Objective fn: 98160.9 Extrapolation: 1 Steplength: 1.58458 Objective fn: 98160.6 Extrapolation: 1 Steplength: 5.74946 Objective fn: 98160.7 Extrapolation: 1 Steplength: 18.0007 Objective fn: 98160.6 Extrapolation: 1 Steplength: 1.31963 Objective fn: 98160.8 Extrapolation: 1 Steplength: 14.5938 Objective fn: 98160.6 Extrapolation: 1 Steplength: 5.87148 Objective fn: 98160.6 Extrapolation: 1 Steplength: 2.79445 Objective fn: 98160.6 Extrapolation: 1 Steplength: 10.536 Objective fn: 98160.6 Extrapolation: 1 Steplength: 1.26176 Objective fn: 98160.6 Extrapolation: 0 Steplength: 1 Objective fn: 98160.6 Extrapolation: 0 Steplength: 1 Objective fn: 98160.6 Extrapolation: 1 Steplength: 64 Objective fn: 98160.7 Extrapolation: 1 Steplength: 11.4375 Objective fn: 98160.6 Extrapolation: 1 Steplength: 3.26847 Objective fn: 98160.6 Extrapolation: 1 Steplength: 4.39932 Objective fn: 98160.6 Extrapolation: 1 Steplength: 3.21355 Objective fn: 98160.6 Extrapolation: 1 Steplength: 7.1878 Objective fn: 98160.6 Extrapolation: 1 Steplength: 1.51531 Objective fn: 98160.5 Extrapolation: 1 Steplength: 256 Objective fn: 98160.5 Extrapolation: 1 Steplength: 1.39451 Objective fn: 98160.7 Extrapolation: 1 Steplength: 479.942 Objective fn: 98160.5 Extrapolation: 1 Steplength: 1.41467 Objective fn: 98160.6 Extrapolation: 1 Steplength: 14.2088 Objective fn: 98160.5 Extrapolation: 1 Steplength: 2.52095 Objective fn: 98160.5 Extrapolation: 1 Steplength: 9.92198 Objective fn: 98160.5 Extrapolation: 1 Steplength: 2.79295</code></pre> <pre><code>Due to absence of package REBayes, switching to EM algorithm</code></pre> <pre><code>Squarem-1 Objective fn: 687462 Objective fn: 233579 Extrapolation: 0 Steplength: 1 Objective fn: 163301 Extrapolation: 1 Steplength: 2.96537 Objective fn: 101350 Extrapolation: 0 Steplength: 1 Objective fn: 87205.9 Extrapolation: 1 Steplength: 3.31731 Objective fn: 83310 Extrapolation: 1 Steplength: 1.41235 Objective fn: 83078.4 Extrapolation: 1 Steplength: 4 Objective fn: 83067.1 Extrapolation: 1 Steplength: 2.82442 Objective fn: 83065.1 Extrapolation: 1 Steplength: 2.48778 Objective fn: 83064.6 Extrapolation: 1 Steplength: 2.94018 Objective fn: 83064.5 Extrapolation: 1 Steplength: 2.28751 Objective fn: 83064.5 Extrapolation: 1 Steplength: 3.24189</code></pre> <pre class="r"><code>bppos = 880001:1011072 plot(bppos,test_matrix[1,]+test_matrix[2,],xlab="position",ylab="counts",pch=16,cex=0.5, col=alpha("black",0.04))</code></pre> <p><img src="figure/test.smash.Rmd/unnamed-chunk-9-1.png" width="672" style="display: block; margin: auto;" /></p> <details> <summary><em>Expand here to see past versions of unnamed-chunk-9-1.png:</em></summary> <table style="border-collapse:separate; border-spacing:5px;"> <thead> <tr> <th style="text-align:left;"> Version </th> <th style="text-align:left;"> Author </th> <th style="text-align:left;"> Date </th> </tr> </thead> <tbody> <tr> <td style="text-align:left;"> <a href="https://github.com/brimittleman/threeprimeseq/blob/0464829eb7efe6e59a1e4c9b119aacf011b4bdaa/docs/figure/test.smash.Rmd/unnamed-chunk-9-1.png" target="_blank">0464829</a> </td> <td style="text-align:left;"> Briana Mittleman </td> <td style="text-align:left;"> 2018-07-17 </td> </tr> </tbody> </table> <p></details></p> <pre class="r"><code>plot(bppos,res$est,type='l',xlab="position",ylab="intensity")</code></pre> <p><img src="figure/test.smash.Rmd/unnamed-chunk-9-2.png" width="672" style="display: block; margin: auto;" /></p> <details> <summary><em>Expand here to see past versions of unnamed-chunk-9-2.png:</em></summary> <table style="border-collapse:separate; border-spacing:5px;"> <thead> <tr> <th style="text-align:left;"> Version </th> <th style="text-align:left;"> Author </th> <th style="text-align:left;"> Date </th> </tr> </thead> <tbody> <tr> <td style="text-align:left;"> <a href="https://github.com/brimittleman/threeprimeseq/blob/0464829eb7efe6e59a1e4c9b119aacf011b4bdaa/docs/figure/test.smash.Rmd/unnamed-chunk-9-2.png" target="_blank">0464829</a> </td> <td style="text-align:left;"> Briana Mittleman </td> <td style="text-align:left;"> 2018-07-17 </td> </tr> </tbody> </table> <p></details></p> <p>Create a coverage file with the results.</p> <pre class="r"><code>cov=cbind(test_18468$chr, test_18468$base + 1, test_18468$base, res$est)</code></pre> </div> <div id="test-actb" class="section level2"> <h2>Test actb</h2> <p>I want to try this on a region with higher background for example where actb is. I can run a smaller region of <span class="math inline">\(2^{10}\)</span> bases. chr7:5,566,662-5,567,686. The following script to extract the region is called test.actbregion.sh.</p> <pre class="bash"><code>#!/bin/bash #SBATCH --job-name=test.regactb #SBATCH --account=pi-yangili1 #SBATCH --time=24:00:00 #SBATCH --output=test.regact.out #SBATCH --error=test.regact.err #SBATCH --partition=broadwl #SBATCH --mem=20G #SBATCH --mail-type=END awk '$1 == 7 && $2 >= 5566662 && $2 <= 5567686 {print}' /project2/gilad/briana/threeprimeseq/data/test.smash/gencov5prime.18486-T_S9_R1_001.bed > /project2/gilad/briana/threeprimeseq/data/test.region/gencov5prime.18486-T_S9_R1_001.testregion.actb.bed awk '$1 == 7 && $2 >= 5566662 && $2 <= 5567686 {print}' /project2/gilad/briana/threeprimeseq/data/test.smash/gencov5prime.18497-T_S11_R1_001.bed > /project2/gilad/briana/threeprimeseq/data/test.region/gencov5prime.18497-T_S11_R1_001.testregion.actb.bed awk '$1 == 7 && $2 >= 5566662 && $2 <= 5567686 {print}' /project2/gilad/briana/threeprimeseq/data/test.smash/gencov5prime.18500-T_S19_R1_001.bed > /project2/gilad/briana/threeprimeseq/data/test.region/gencov5prime.18500-T_S19_R1_001.testregion.actb.bed awk '$1 == 7 && $2 >= 5566662 && $2 <= 5567686 {print}' /project2/gilad/briana/threeprimeseq/data/test.smash/gencov5prime.18505-T_S1_R1_001.bed > /project2/gilad/briana/threeprimeseq/data/test.region/gencov5prime.18505-T_S1_R1_001.testregion.actb.bed awk '$1 == 7 && $2 >= 5566662 && $2 <= 5567686 {print}' /project2/gilad/briana/threeprimeseq/data/test.smash/gencov5prime.18508-T_S5_R1_001.bed > /project2/gilad/briana/threeprimeseq/data/test.region/gencov5prime.18508-T_S5_R1_001.testregion.actb.bed awk '$1 == 7 && $2 >= 5566662 && $2 <= 5567686 {print}' /project2/gilad/briana/threeprimeseq/data/test.smash/gencov5prime.18853-T_S31_R1_001.bed > /project2/gilad/briana/threeprimeseq/data/test.region/gencov5prime.18853-T_S31_R1_001.testregion.actb.bed awk '$1 == 7 && $2 >= 5566662 && $2 <= 5567686 {print}' /project2/gilad/briana/threeprimeseq/data/test.smash/gencov5prime.18870-T_S23_R1_001.bed > /project2/gilad/briana/threeprimeseq/data/test.region/gencov5prime.18870-T_S23_R1_001.testregion.actb.bed awk '$1 == 7 && $2 >= 5566662 && $2 <= 5567686 {print}' /project2/gilad/briana/threeprimeseq/data/test.smash/gencov5prime.19128-T_S29_R1_001.bed > /project2/gilad/briana/threeprimeseq/data/test.region/gencov5prime.19128-T_S29_R1_001.testregion.actb.bed awk '$1 == 7 && $2 >= 5566662 && $2 <= 5567686 {print}' /project2/gilad/briana/threeprimeseq/data/test.smash/gencov5prime.19141-T_S17_R1_001.bed > /project2/gilad/briana/threeprimeseq/data/test.region/gencov5prime.19141-T_S17_R1_001.testregion.actb.bed awk '$1 == 7 && $2 >= 5566662 && $2 <= 5567686 {print}' /project2/gilad/briana/threeprimeseq/data/test.smash/gencov5prime.19193-T_S21_R1_001.bed > /project2/gilad/briana/threeprimeseq/data/test.region/gencov5prime.19193-T_S21_R1_001.testregion.actb.bed awk '$1 == 7 && $2 >= 5566662 && $2 <= 5567686 {print}' /project2/gilad/briana/threeprimeseq/data/test.smash/gencov5prime.19209-T_S15_R1_001.bed > /project2/gilad/briana/threeprimeseq/data/test.region/gencov5prime.19209-T_S15_R1_001.testregion.actb.bed awk '$1 == 7 && $2 >= 5566662 && $2 <= 5567686 {print}' /project2/gilad/briana/threeprimeseq/data/test.smash/gencov5prime.19233-T_S7_R1_001.bed > /project2/gilad/briana/threeprimeseq/data/test.region/gencov5prime.19223-T_S7_R1_001.testregion.actb.bed awk '$1 == 7 && $2 >= 5566662 && $2 <= 5567686 {print}' /project2/gilad/briana/threeprimeseq/data/test.smash/gencov5prime.19225-T_S27_R1_001.bed > /project2/gilad/briana/threeprimeseq/data/test.region/gencov5prime.19225-T_S27_R1_001.testregion.actb.bed awk '$1 == 7 && $2 >= 5566662 && $2 <= 5567686 {print}' /project2/gilad/briana/threeprimeseq/data/test.smash/gencov5prime.19238-T_S3_R1_001.bed > /project2/gilad/briana/threeprimeseq/data/test.region/gencov5prime.19238-T_S3_R1_001.testregion.actb.bed awk '$1 == 7 && $2 >= 5566662 && $2 <= 5567686 {print}' /project2/gilad/briana/threeprimeseq/data/test.smash/gencov5prime.19239-T_S13_R1_001.bed > /project2/gilad/briana/threeprimeseq/data/test.region/gencov5prime.19239-T_S13_R1_001.testregion.actb.bed awk '$1 == 7 && $2 >= 5566662 && $2 <= 5567686 {print}' /project2/gilad/briana/threeprimeseq/data/test.smash/gencov5prime.19257-T_S25_R1_001.bed > /project2/gilad/briana/threeprimeseq/data/test.region/gencov5prime.19257-T_S25_R1_001.testregion.actb.bed </code></pre> <p>18853 did not work, running seperatly.</p> <pre class="r"><code>actb_test_18468=read.table("../data/smash_testregion/gencov5prime.18486-T_S9_R1_001.testregion.actb.bed", col.names=c("chr", "base", "T18486")) actb_test_18497=read.table("../data/smash_testregion/gencov5prime.18497-T_S11_R1_001.testregion.actb.bed", col.names=c("chr", "base", "T18497")) actb_test_18500=read.table("../data/smash_testregion/gencov5prime.18500-T_S19_R1_001.testregion.actb.bed", col.names=c("chr", "base", "T18500")) actb_test_18505=read.table("../data/smash_testregion/gencov5prime.18505-T_S1_R1_001.testregion.actb.bed", col.names=c("chr", "base", "T18505")) actb_test_18508=read.table("../data/smash_testregion/gencov5prime.18508-T_S5_R1_001.testregion.actb.bed", col.names=c("chr", "base", "T18508")) actb_test_18853=read.table("../data/smash_testregion/gencov5prime.18853-T_S31_R1_001.testregion.actb.bed", col.names=c("chr", "base", "T18853")) actb_test_18870=read.table("../data/smash_testregion/gencov5prime.18870-T_S23_R1_001.testregion.actb.bed", col.names=c("chr", "base", "T18870")) actb_test_19128=read.table("../data/smash_testregion/gencov5prime.19128-T_S29_R1_001.testregion.actb.bed", col.names=c("chr", "base", "T19128")) actb_test_19239=read.table("../data/smash_testregion/gencov5prime.19239-T_S13_R1_001.testregion.actb.bed", col.names=c("chr", "base", "T19239")) actb_test_19257=read.table("../data/smash_testregion/gencov5prime.19257-T_S25_R1_001.testregion.actb.bed", col.names=c("chr", "base", "T19257")) actb_test_19141=read.table("../data/smash_testregion/gencov5prime.19141-T_S17_R1_001.testregion.actb.bed", col.names=c("chr", "base", "T19141")) actb_test_19193=read.table("../data/smash_testregion/gencov5prime.19193-T_S21_R1_001.testregion.actb.bed", col.names=c("chr", "base", "T19193")) actb_test_19209=read.table("../data/smash_testregion/gencov5prime.19209-T_S15_R1_001.testregion.actb.bed", col.names=c("chr", "base", "T19209")) actb_test_19223=read.table("../data/smash_testregion/gencov5prime.19223-T_S7_R1_001.testregion.actb.bed", col.names=c("chr", "base", "T19223")) actb_test_19225=read.table("../data/smash_testregion/gencov5prime.19225-T_S27_R1_001.testregion.actb.bed", col.names=c("chr", "base", "T19225")) actb_test_19238=read.table("../data/smash_testregion/gencov5prime.19238-T_S3_R1_001.testregion.actb.bed", col.names=c("chr", "base", "T19238"))</code></pre> <p>Make matrix</p> <pre class="r"><code>actb_test_matrix=cbind(actb_test_18468$T18486, actb_test_18497$T18497, actb_test_18500$T18500, actb_test_18505$T18505, actb_test_18508$T18508, actb_test_18853$T18853, actb_test_18870$T18870, actb_test_19128$T19128, actb_test_19141$T19141, actb_test_19193$T19193, actb_test_19209$T19209, actb_test_19223$T19223, actb_test_19225$T19225, actb_test_19238$T19238, actb_test_19239$T19239, actb_test_19257$T19257) %>% t</code></pre> <p>Run smash:</p> <pre class="r"><code>actb_res = smash.poiss(actb_test_matrix[1,]+actb_test_matrix[2,]+ actb_test_matrix[3,]+actb_test_matrix[4,]+actb_test_matrix[5,]+actb_test_matrix[6,]+actb_test_matrix[7,]+actb_test_matrix[8,]+actb_test_matrix[9,]+actb_test_matrix[10,]+actb_test_matrix[11,]+actb_test_matrix[12,]+actb_test_matrix[13,]+actb_test_matrix[14,]+actb_test_matrix[15,]+actb_test_matrix[16,],post.var=TRUE)</code></pre> <pre><code>Due to absence of package REBayes, switching to EM algorithm Due to absence of package REBayes, switching to EM algorithm Due to absence of package REBayes, switching to EM algorithm Due to absence of package REBayes, switching to EM algorithm Due to absence of package REBayes, switching to EM algorithm Due to absence of package REBayes, switching to EM algorithm Due to absence of package REBayes, switching to EM algorithm Due to absence of package REBayes, switching to EM algorithm Due to absence of package REBayes, switching to EM algorithm Due to absence of package REBayes, switching to EM algorithm Due to absence of package REBayes, switching to EM algorithm Due to absence of package REBayes, switching to EM algorithm</code></pre> <p>Make plots:</p> <pre class="r"><code>actb_bppos = 5566662:5567686 plot(actb_bppos,actb_test_matrix[1,]+actb_test_matrix[2,]+ actb_test_matrix[3,]+actb_test_matrix[4,]+actb_test_matrix[5,]+actb_test_matrix[6,]+actb_test_matrix[7,]+actb_test_matrix[8,]+actb_test_matrix[9,]+actb_test_matrix[10,]+actb_test_matrix[11,]+actb_test_matrix[12,]+actb_test_matrix[13,]+actb_test_matrix[14,]+actb_test_matrix[15,]+actb_test_matrix[16,],xlab="position",ylab="counts",pch=16,cex=0.5, col=alpha("black",.5), main="Raw data ACTB")</code></pre> <p><img src="figure/test.smash.Rmd/unnamed-chunk-15-1.png" width="672" style="display: block; margin: auto;" /></p> <details> <summary><em>Expand here to see past versions of unnamed-chunk-15-1.png:</em></summary> <table style="border-collapse:separate; border-spacing:5px;"> <thead> <tr> <th style="text-align:left;"> Version </th> <th style="text-align:left;"> Author </th> <th style="text-align:left;"> Date </th> </tr> </thead> <tbody> <tr> <td style="text-align:left;"> <a href="https://github.com/brimittleman/threeprimeseq/blob/652b7e9a399ef80fef98e1a7943cd2224b154c9a/docs/figure/test.smash.Rmd/unnamed-chunk-15-1.png" target="_blank">652b7e9</a> </td> <td style="text-align:left;"> Briana Mittleman </td> <td style="text-align:left;"> 2018-07-19 </td> </tr> <tr> <td style="text-align:left;"> <a href="https://github.com/brimittleman/threeprimeseq/blob/319322373c1d7d83d53b6eb868a5fefae3dd682d/docs/figure/test.smash.Rmd/unnamed-chunk-15-1.png" target="_blank">3193223</a> </td> <td style="text-align:left;"> Briana Mittleman </td> <td style="text-align:left;"> 2018-07-18 </td> </tr> </tbody> </table> <p></details></p> <pre class="r"><code>plot(actb_bppos,actb_res$est,type='l',xlab="position",ylab="intensity", main="SMASH results ACTB")</code></pre> <p><img src="figure/test.smash.Rmd/unnamed-chunk-15-2.png" width="672" style="display: block; margin: auto;" /></p> <details> <summary><em>Expand here to see past versions of unnamed-chunk-15-2.png:</em></summary> <table style="border-collapse:separate; border-spacing:5px;"> <thead> <tr> <th style="text-align:left;"> Version </th> <th style="text-align:left;"> Author </th> <th style="text-align:left;"> Date </th> </tr> </thead> <tbody> <tr> <td style="text-align:left;"> <a href="https://github.com/brimittleman/threeprimeseq/blob/652b7e9a399ef80fef98e1a7943cd2224b154c9a/docs/figure/test.smash.Rmd/unnamed-chunk-15-2.png" target="_blank">652b7e9</a> </td> <td style="text-align:left;"> Briana Mittleman </td> <td style="text-align:left;"> 2018-07-19 </td> </tr> <tr> <td style="text-align:left;"> <a href="https://github.com/brimittleman/threeprimeseq/blob/319322373c1d7d83d53b6eb868a5fefae3dd682d/docs/figure/test.smash.Rmd/unnamed-chunk-15-2.png" target="_blank">3193223</a> </td> <td style="text-align:left;"> Briana Mittleman </td> <td style="text-align:left;"> 2018-07-18 </td> </tr> </tbody> </table> <p></details></p> </div> <div id="test-gapdh" class="section level2"> <h2>Test Gapdh</h2> <p>Check on another highly expressed gene to see if this dual peak pattern appears again. I will look at GAPDH. Chr12 6,646,755-6,647,779</p> <pre class="bash"><code>#!/bin/bash #SBATCH --job-name=test.reggap #SBATCH --account=pi-yangili1 #SBATCH --time=24:00:00 #SBATCH --output=test.reggap.out #SBATCH --error=test.reggap.err #SBATCH --partition=broadwl #SBATCH --mem=20G #SBATCH --mail-type=END awk '$1 == 12 && $2 >= 6646755 && $2 <= 6647779 {print}' /project2/gilad/briana/threeprimeseq/data/test.smash/gencov5prime.18486-T_S9_R1_001.bed > /project2/gilad/briana/threeprimeseq/data/test.region/gencov5prime.18486-T_S9_R1_001.testregion.gap.bed awk '$1 == 12 && $2 >= 6646755 && $2 <= 6647779 {print}' /project2/gilad/briana/threeprimeseq/data/test.smash/gencov5prime.18497-T_S11_R1_001.bed > /project2/gilad/briana/threeprimeseq/data/test.region/gencov5prime.18497-T_S11_R1_001.testregion.gap.bed awk '$1 == 12 && $2 >= 6646755 && $2 <= 6647779 {print}' /project2/gilad/briana/threeprimeseq/data/test.smash/gencov5prime.18500-T_S19_R1_001.bed > /project2/gilad/briana/threeprimeseq/data/test.region/gencov5prime.18500-T_S19_R1_001.testregion.gap.bed awk '$1 == 12 && $2 >= 6646755 && $2 <= 6647779 {print}' /project2/gilad/briana/threeprimeseq/data/test.smash/gencov5prime.18505-T_S1_R1_001.bed > /project2/gilad/briana/threeprimeseq/data/test.region/gencov5prime.18505-T_S1_R1_001.testregion.gap.bed awk '$1 == 12 && $2 >= 6646755 && $2 <= 6647779 {print}' /project2/gilad/briana/threeprimeseq/data/test.smash/gencov5prime.18508-T_S5_R1_001.bed > /project2/gilad/briana/threeprimeseq/data/test.region/gencov5prime.18508-T_S5_R1_001.testregion.gap.bed awk '$1 == 12 && $2 >= 6646755 && $2 <= 6647779 {print}' /project2/gilad/briana/threeprimeseq/data/test.smash/gencov5prime.18853-T_S31_R1_001.bed > /project2/gilad/briana/threeprimeseq/data/test.region/gencov5prime.18853-T_S31_R1_001.testregion.gap.bed awk '$1 == 12 && $2 >= 6646755 && $2 <= 6647779 {print}' /project2/gilad/briana/threeprimeseq/data/test.smash/gencov5prime.18870-T_S23_R1_001.bed > /project2/gilad/briana/threeprimeseq/data/test.region/gencov5prime.18870-T_S23_R1_001.testregion.gap.bed awk '$1 == 12 && $2 >= 6646755 && $2 <= 6647779 {print}' /project2/gilad/briana/threeprimeseq/data/test.smash/gencov5prime.19128-T_S29_R1_001.bed > /project2/gilad/briana/threeprimeseq/data/test.region/gencov5prime.19128-T_S29_R1_001.testregion.gap.bed awk '$1 == 12 && $2 >= 6646755 && $2 <= 6647779 {print}' /project2/gilad/briana/threeprimeseq/data/test.smash/gencov5prime.19141-T_S17_R1_001.bed > /project2/gilad/briana/threeprimeseq/data/test.region/gencov5prime.19141-T_S17_R1_001.testregion.gap.bed awk '$1 == 12 && $2 >= 6646755 && $2 <= 6647779 {print}' /project2/gilad/briana/threeprimeseq/data/test.smash/gencov5prime.19193-T_S21_R1_001.bed > /project2/gilad/briana/threeprimeseq/data/test.region/gencov5prime.19193-T_S21_R1_001.testregion.gap.bed awk '$1 == 12 && $2 >= 6646755 && $2 <= 6647779 {print}' /project2/gilad/briana/threeprimeseq/data/test.smash/gencov5prime.19209-T_S15_R1_001.bed > /project2/gilad/briana/threeprimeseq/data/test.region/gencov5prime.19209-T_S15_R1_001.testregion.gap.bed awk '$1 == 12 && $2 >= 6646755 && $2 <= 6647779 {print}' /project2/gilad/briana/threeprimeseq/data/test.smash/gencov5prime.19233-T_S7_R1_001.bed > /project2/gilad/briana/threeprimeseq/data/test.region/gencov5prime.19223-T_S7_R1_001.testregion.gap.bed awk '$1 == 12 && $2 >= 6646755 && $2 <= 6647779 {print}' /project2/gilad/briana/threeprimeseq/data/test.smash/gencov5prime.19225-T_S27_R1_001.bed > /project2/gilad/briana/threeprimeseq/data/test.region/gencov5prime.19225-T_S27_R1_001.testregion.gap.bed awk '$1 == 12 && $2 >= 6646755 && $2 <= 6647779 {print}' /project2/gilad/briana/threeprimeseq/data/test.smash/gencov5prime.19238-T_S3_R1_001.bed > /project2/gilad/briana/threeprimeseq/data/test.region/gencov5prime.19238-T_S3_R1_001.testregion.gap.bed awk '$1 == 12 && $2 >= 6646755 && $2 <= 6647779 {print}' /project2/gilad/briana/threeprimeseq/data/test.smash/gencov5prime.19239-T_S13_R1_001.bed > /project2/gilad/briana/threeprimeseq/data/test.region/gencov5prime.19239-T_S13_R1_001.testregion.gap.bed awk '$1 == 12 && $2 >= 6646755 && $2 <= 6647779 {print}' /project2/gilad/briana/threeprimeseq/data/test.smash/gencov5prime.19257-T_S25_R1_001.bed > /project2/gilad/briana/threeprimeseq/data/test.region/gencov5prime.19257-T_S25_R1_001.testregion.gap.bed </code></pre> <p>Pull in the data:</p> <pre class="r"><code>gap_test_18468=read.table("../data/smash_testregion/gencov5prime.18486-T_S9_R1_001.testregion.gap.bed", col.names=c("chr", "base", "T18486")) gap_test_18497=read.table("../data/smash_testregion/gencov5prime.18497-T_S11_R1_001.testregion.gap.bed", col.names=c("chr", "base", "T18497")) gap_test_18500=read.table("../data/smash_testregion/gencov5prime.18500-T_S19_R1_001.testregion.gap.bed", col.names=c("chr", "base", "T18500")) gap_test_18505=read.table("../data/smash_testregion/gencov5prime.18505-T_S1_R1_001.testregion.gap.bed", col.names=c("chr", "base", "T18505")) gap_test_18508=read.table("../data/smash_testregion/gencov5prime.18508-T_S5_R1_001.testregion.gap.bed", col.names=c("chr", "base", "T18508")) gap_test_18853=read.table("../data/smash_testregion/gencov5prime.18853-T_S31_R1_001.testregion.gap.bed", col.names=c("chr", "base", "T18853")) gap_test_18870=read.table("../data/smash_testregion/gencov5prime.18870-T_S23_R1_001.testregion.gap.bed", col.names=c("chr", "base", "T18870")) gap_test_19128=read.table("../data/smash_testregion/gencov5prime.19128-T_S29_R1_001.testregion.gap.bed", col.names=c("chr", "base", "T19128")) gap_test_19239=read.table("../data/smash_testregion/gencov5prime.19239-T_S13_R1_001.testregion.gap.bed", col.names=c("chr", "base", "T19239")) gap_test_19257=read.table("../data/smash_testregion/gencov5prime.19257-T_S25_R1_001.testregion.gap.bed", col.names=c("chr", "base", "T19257")) gap_test_19141=read.table("../data/smash_testregion/gencov5prime.19141-T_S17_R1_001.testregion.gap.bed", col.names=c("chr", "base", "T19141")) gap_test_19193=read.table("../data/smash_testregion/gencov5prime.19193-T_S21_R1_001.testregion.gap.bed", col.names=c("chr", "base", "T19193")) gap_test_19209=read.table("../data/smash_testregion/gencov5prime.19209-T_S15_R1_001.testregion.gap.bed", col.names=c("chr", "base", "T19209")) gap_test_19223=read.table("../data/smash_testregion/gencov5prime.19223-T_S7_R1_001.testregion.gap.bed", col.names=c("chr", "base", "T19223")) gap_test_19225=read.table("../data/smash_testregion/gencov5prime.19225-T_S27_R1_001.testregion.gap.bed", col.names=c("chr", "base", "T19225")) gap_test_19238=read.table("../data/smash_testregion/gencov5prime.19238-T_S3_R1_001.testregion.gap.bed", col.names=c("chr", "base", "T19238"))</code></pre> <p>Make matrix</p> <pre class="r"><code>gap_test_matrix=cbind(gap_test_18468$T18486, gap_test_18497$T18497, gap_test_18500$T18500, gap_test_18505$T18505, gap_test_18508$T18508, gap_test_18853$T18853, gap_test_18870$T18870, gap_test_19128$T19128, gap_test_19141$T19141, gap_test_19193$T19193, gap_test_19209$T19209, gap_test_19223$T19223, gap_test_19225$T19225, gap_test_19238$T19238, gap_test_19239$T19239, gap_test_19257$T19257) %>% t</code></pre> <p>Run smash:</p> <pre class="r"><code>gap_res = smash.poiss(gap_test_matrix[1,]+gap_test_matrix[2,]+gap_test_matrix[3,]+gap_test_matrix[4,]+gap_test_matrix[5,]+gap_test_matrix[6,]+gap_test_matrix[7,]+gap_test_matrix[8,]+gap_test_matrix[9,]+gap_test_matrix[10,]+gap_test_matrix[11,]+gap_test_matrix[12,]+gap_test_matrix[13,]+gap_test_matrix[14,]+gap_test_matrix[15,]+gap_test_matrix[15,]+ gap_test_matrix[16,],post.var=TRUE)</code></pre> <pre><code>Due to absence of package REBayes, switching to EM algorithm Due to absence of package REBayes, switching to EM algorithm Due to absence of package REBayes, switching to EM algorithm Due to absence of package REBayes, switching to EM algorithm Due to absence of package REBayes, switching to EM algorithm Due to absence of package REBayes, switching to EM algorithm Due to absence of package REBayes, switching to EM algorithm Due to absence of package REBayes, switching to EM algorithm Due to absence of package REBayes, switching to EM algorithm Due to absence of package REBayes, switching to EM algorithm Due to absence of package REBayes, switching to EM algorithm Due to absence of package REBayes, switching to EM algorithm</code></pre> <p>Make plots:</p> <pre class="r"><code>gap_bppos =6646755:6647779 plot(gap_test_matrix[1,]+gap_test_matrix[2,]+gap_test_matrix[3,]+gap_test_matrix[4,]+gap_test_matrix[5,]+gap_test_matrix[6,]+gap_test_matrix[7,]+gap_test_matrix[8,]+gap_test_matrix[9,]+gap_test_matrix[10,]+gap_test_matrix[11,]+gap_test_matrix[12,]+gap_test_matrix[13,]+gap_test_matrix[14,]+gap_test_matrix[15,]+gap_test_matrix[15,]+ gap_test_matrix[16,],xlab="position",ylab="counts",pch=16,cex=0.5, col=alpha("black",.5), main="Raw data GAPDH")</code></pre> <p><img src="figure/test.smash.Rmd/unnamed-chunk-20-1.png" width="672" style="display: block; margin: auto;" /></p> <details> <summary><em>Expand here to see past versions of unnamed-chunk-20-1.png:</em></summary> <table style="border-collapse:separate; border-spacing:5px;"> <thead> <tr> <th style="text-align:left;"> Version </th> <th style="text-align:left;"> Author </th> <th style="text-align:left;"> Date </th> </tr> </thead> <tbody> <tr> <td style="text-align:left;"> <a href="https://github.com/brimittleman/threeprimeseq/blob/652b7e9a399ef80fef98e1a7943cd2224b154c9a/docs/figure/test.smash.Rmd/unnamed-chunk-20-1.png" target="_blank">652b7e9</a> </td> <td style="text-align:left;"> Briana Mittleman </td> <td style="text-align:left;"> 2018-07-19 </td> </tr> </tbody> </table> <p></details></p> <pre class="r"><code>plot(gap_bppos,gap_res$est,type='l',xlab="position",ylab="intensity", main="SMASH results GAPDH")</code></pre> <p><img src="figure/test.smash.Rmd/unnamed-chunk-20-2.png" width="672" style="display: block; margin: auto;" /></p> <details> <summary><em>Expand here to see past versions of unnamed-chunk-20-2.png:</em></summary> <table style="border-collapse:separate; border-spacing:5px;"> <thead> <tr> <th style="text-align:left;"> Version </th> <th style="text-align:left;"> Author </th> <th style="text-align:left;"> Date </th> </tr> </thead> <tbody> <tr> <td style="text-align:left;"> <a href="https://github.com/brimittleman/threeprimeseq/blob/652b7e9a399ef80fef98e1a7943cd2224b154c9a/docs/figure/test.smash.Rmd/unnamed-chunk-20-2.png" target="_blank">652b7e9</a> </td> <td style="text-align:left;"> Briana Mittleman </td> <td style="text-align:left;"> 2018-07-19 </td> </tr> </tbody> </table> <p></details></p> </div> <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] dplyr_0.7.5 workflowr_1.0.1 rmarkdown_1.8.5 tidyr_0.7.2 [5] smashr_1.2-0 scales_0.5.0 devtools_1.13.6 loaded via a namespace (and not attached): [1] Rcpp_0.12.17 bindr_0.1.1 pillar_1.1.0 [4] compiler_3.4.2 git2r_0.21.0 plyr_1.8.4 [7] R.methodsS3_1.7.1 R.utils_2.6.0 bitops_1.0-6 [10] iterators_1.0.10 tools_3.4.2 digest_0.6.15 [13] tibble_1.4.2 evaluate_0.10.1 memoise_1.1.0 [16] lattice_0.20-35 pkgconfig_2.0.1 rlang_0.2.1 [19] Matrix_1.2-12 foreach_1.4.4 yaml_2.1.19 [22] parallel_3.4.2 bindrcpp_0.2.2 withr_2.1.1 [25] stringr_1.3.1 knitr_1.18 caTools_1.17.1 [28] tidyselect_0.2.4 rprojroot_1.3-2 grid_3.4.2 [31] glue_1.2.0 data.table_1.11.4 R6_2.2.2 [34] purrr_0.2.5 ashr_2.2-7 magrittr_1.5 [37] whisker_0.3-2 backports_1.1.2 codetools_0.2-15 [40] htmltools_0.3.6 MASS_7.3-48 assertthat_0.2.0 [43] colorspace_1.3-2 wavethresh_4.6.8 stringi_1.2.2 [46] munsell_0.4.3 doParallel_1.0.11 pscl_1.5.2 [49] truncnorm_1.0-8 SQUAREM_2017.10-1 R.oo_1.22.0 </code></pre> </div> <hr> <p> </p> <hr> <!-- To enable disqus, uncomment the section below and provide your disqus_shortname --> <!-- disqus <div id="disqus_thread"></div> <script type="text/javascript"> /* * * CONFIGURATION VARIABLES: EDIT BEFORE PASTING INTO YOUR WEBPAGE * * */ var disqus_shortname = 'rmarkdown'; // required: replace example with your forum shortname /* * * DON'T EDIT BELOW THIS LINE * * */ (function() { var dsq = document.createElement('script'); dsq.type = 'text/javascript'; dsq.async = true; dsq.src = '//' + disqus_shortname + '.disqus.com/embed.js'; 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