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<!DOCTYPE html>
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<ul>
<li><a href="#figure-3d-max-chip-nexus-profiles-at-ebox-variants">Figure 3D: Max ChIP-nexus profiles at EBOX variants</a><ul>
<li><a href="#overview">Overview</a></li>
<li><a href="#motif-variants">Motif variants</a></li>
<li><a href="#session-information">Session information</a></li>
</ul></li>
</ul>
</div>
<div id="figure-3d-max-chip-nexus-profiles-at-ebox-variants" class="section level1">
<h1>Figure 3D: Max ChIP-nexus profiles at EBOX variants</h1>
<p><strong>Project:</strong> ChIP-nexus methods paper</p>
<p><strong>Author:</strong> <a href="mailto:[email protected]">Jeff Johnston</a></p>
<p><strong>Generated:</strong> Thu Dec 04 2014, 03:22 PM</p>
<div id="overview" class="section level2">
<h2>Overview</h2>
<p>We will compare the profiles of the following samples around the top 200 EBOX motifs per variant:</p>
<!-- html table generated in R 3.1.1 by xtable 1.7-4 package -->
<!-- Thu Dec 4 15:22:15 2014 -->
<table border="1">
<tr>
<th>
sample
</th>
<th>
antibody
</th>
<th>
species
</th>
<th>
digestion
</th>
</tr>
<tr>
<td>
dmel_s2_max_chipnexus_01
</td>
<td>
max
</td>
<td>
dmel
</td>
<td>
lambda
</td>
</tr>
<tr>
<td>
dmel_s2_max_chipnexus_02
</td>
<td>
max
</td>
<td>
dmel
</td>
<td>
lambda
</td>
</tr>
</table>
</div>
<div id="motif-variants" class="section level2">
<h2>Motif variants</h2>
<!-- html table generated in R 3.1.1 by xtable 1.7-4 package -->
<!-- Thu Dec 4 15:22:15 2014 -->
<table border="1">
<tr>
<th>
motif_name
</th>
<th>
sequence
</th>
</tr>
<tr>
<td>
AA/TT
</td>
<td>
CAAATG
</td>
</tr>
<tr>
<td>
AC/GT
</td>
<td>
CAACTG
</td>
</tr>
<tr>
<td>
AG/CT
</td>
<td>
CAAGTG
</td>
</tr>
<tr>
<td>
AT
</td>
<td>
CAATTG
</td>
</tr>
<tr>
<td>
CA/TG
</td>
<td>
CACATG
</td>
</tr>
<tr>
<td>
CC/GG
</td>
<td>
CACCTG
</td>
</tr>
<tr>
<td>
CG
</td>
<td>
CACGTG
</td>
</tr>
<tr>
<td>
GA/TC
</td>
<td>
CAGATG
</td>
</tr>
<tr>
<td>
GC
</td>
<td>
CAGCTG
</td>
</tr>
<tr>
<td>
TA
</td>
<td>
CATATG
</td>
</tr>
</table>
<p><img src="figure_3_d_max_ebox_output/plots_per_sample-1.png" title="" alt="" width="1200" /><img src="figure_3_d_max_ebox_output/plots_per_sample-2.png" title="" alt="" width="1200" /></p>
</div>
<div id="session-information" class="section level2">
<h2>Session information</h2>
<p>For reproducibility, this analysis was performed with the following R/Bioconductor session:</p>
<pre><code>R version 3.1.1 (2014-07-10)
Platform: x86_64-pc-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] grid stats4 parallel stats graphics grDevices utils
[8] datasets methods base
other attached packages:
[1] lattice_0.20-29 reshape2_1.4
[3] digest_0.6.4 yaml_2.1.13
[5] BSgenome.Dmelanogaster.UCSC.dm3_1.4.0 BSgenome_1.34.0
[7] rtracklayer_1.26.1 Biostrings_2.34.0
[9] XVector_0.6.0 GenomicRanges_1.18.1
[11] GenomeInfoDb_1.2.0 IRanges_2.0.0
[13] S4Vectors_0.4.0 BiocGenerics_0.12.0
[15] plyr_1.8.1 ggplot2_1.0.0
[17] xtable_1.7-4
loaded via a namespace (and not attached):
[1] base64enc_0.1-2 BatchJobs_1.4 BBmisc_1.7
[4] BiocParallel_1.0.0 bitops_1.0-6 brew_1.0-6
[7] checkmate_1.5.0 codetools_0.2-9 colorspace_1.2-4
[10] DBI_0.3.1 evaluate_0.5.5 fail_1.2
[13] foreach_1.4.2 formatR_1.0 GenomicAlignments_1.2.0
[16] gtable_0.1.2 htmltools_0.2.6 iterators_1.0.7
[19] knitr_1.7 labeling_0.3 MASS_7.3-35
[22] munsell_0.4.2 proto_0.3-10 Rcpp_0.11.3
[25] RCurl_1.95-4.3 rmarkdown_0.3.3 Rsamtools_1.18.0
[28] RSQLite_0.11.4 scales_0.2.4 sendmailR_1.2-1
[31] stringr_0.6.2 tools_3.1.1 XML_3.98-1.1
[34] zlibbioc_1.12.0 </code></pre>
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