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<!DOCTYPE html>
<html lang="" xml:lang="">
<head>
<meta charset="utf-8" />
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<title>S7 POE HPTM enrichment-POE transcription dynamics | Supplementary Materials: Intragenomic conflict underlies extreme phenotypic plasticity in queen-worker caste determination in honey bees (Apis mellifera)</title>
<meta name="description" content="S7 POE HPTM enrichment-POE transcription dynamics | Supplementary Materials: Intragenomic conflict underlies extreme phenotypic plasticity in queen-worker caste determination in honey bees (Apis mellifera)" />
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<meta property="og:title" content="S7 POE HPTM enrichment-POE transcription dynamics | Supplementary Materials: Intragenomic conflict underlies extreme phenotypic plasticity in queen-worker caste determination in honey bees (Apis mellifera)" />
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<meta name="twitter:title" content="S7 POE HPTM enrichment-POE transcription dynamics | Supplementary Materials: Intragenomic conflict underlies extreme phenotypic plasticity in queen-worker caste determination in honey bees (Apis mellifera)" />
<meta name="author" content="Sean T. Bresnahan, Shaun Mahony, Kate Anton, Brock Harpur, Christina M. Grozinger" />
<meta name="date" content="2024-06-09" />
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<body>
<div class="book without-animation with-summary font-size-2 font-family-1" data-basepath=".">
<div class="book-summary">
<nav role="navigation">
<ul class="summary">
<li><a href="./">Appendix D</a></li>
<li class="divider"></li>
<li><a href="index.html#section" id="toc-section"></a></li>
<li class="chapter" data-level="1" data-path="wgs-mrna-seq-and-chip-seq.html"><a href="wgs-mrna-seq-and-chip-seq.html"><i class="fa fa-check"></i><b>1</b> WGS, mRNA-seq, and ChIP-seq</a>
<ul>
<li class="chapter" data-level="1.1" data-path="wgs-mrna-seq-and-chip-seq.html"><a href="wgs-mrna-seq-and-chip-seq.html#wgs"><i class="fa fa-check"></i><b>1.1</b> WGS</a></li>
<li class="chapter" data-level="1.2" data-path="wgs-mrna-seq-and-chip-seq.html"><a href="wgs-mrna-seq-and-chip-seq.html#mrna-seq"><i class="fa fa-check"></i><b>1.2</b> mRNA-seq</a></li>
<li class="chapter" data-level="1.3" data-path="wgs-mrna-seq-and-chip-seq.html"><a href="wgs-mrna-seq-and-chip-seq.html#chip-seq"><i class="fa fa-check"></i><b>1.3</b> ChIP-seq</a></li>
</ul></li>
<li class="chapter" data-level="2" data-path="transcriptomic-analyses.html"><a href="transcriptomic-analyses.html"><i class="fa fa-check"></i><b>2</b> Transcriptomic Analyses</a>
<ul>
<li class="chapter" data-level="2.1" data-path="transcriptomic-analyses.html"><a href="transcriptomic-analyses.html#differential-gene-expression-analysis"><i class="fa fa-check"></i><b>2.1</b> Differential gene expression analysis</a></li>
<li class="chapter" data-level="2.2" data-path="transcriptomic-analyses.html"><a href="transcriptomic-analyses.html#wgcna"><i class="fa fa-check"></i><b>2.2</b> WGCNA</a></li>
</ul></li>
<li class="chapter" data-level="3" data-path="allele-specific-transcriptomic-analyses.html"><a href="allele-specific-transcriptomic-analyses.html"><i class="fa fa-check"></i><b>3</b> Allele-Specific Transcriptomic Analyses</a>
<ul>
<li class="chapter" data-level="3.1" data-path="allele-specific-transcriptomic-analyses.html"><a href="allele-specific-transcriptomic-analyses.html#snps-and-transcripts"><i class="fa fa-check"></i><b>3.1</b> SNPs and transcripts</a></li>
<li class="chapter" data-level="3.2" data-path="allele-specific-transcriptomic-analyses.html"><a href="allele-specific-transcriptomic-analyses.html#poe-gene-lists"><i class="fa fa-check"></i><b>3.2</b> POE gene lists</a></li>
<li class="chapter" data-level="3.3" data-path="allele-specific-transcriptomic-analyses.html"><a href="allele-specific-transcriptomic-analyses.html#hpf-wl-ql---allelic-transcriptomics"><i class="fa fa-check"></i><b>3.3</b> 192hpf WL & QL - allelic transcriptomics</a>
<ul>
<li class="chapter" data-level="3.3.1" data-path="allele-specific-transcriptomic-analyses.html"><a href="allele-specific-transcriptomic-analyses.html#block-1"><i class="fa fa-check"></i><b>3.3.1</b> Block 1</a></li>
<li class="chapter" data-level="3.3.2" data-path="allele-specific-transcriptomic-analyses.html"><a href="allele-specific-transcriptomic-analyses.html#block-2"><i class="fa fa-check"></i><b>3.3.2</b> Block 2</a></li>
</ul></li>
<li class="chapter" data-level="3.4" data-path="allele-specific-transcriptomic-analyses.html"><a href="allele-specific-transcriptomic-analyses.html#hpf-eggs---allelic-transcriptomics"><i class="fa fa-check"></i><b>3.4</b> 24hpf eggs - allelic transcriptomics</a>
<ul>
<li class="chapter" data-level="3.4.1" data-path="allele-specific-transcriptomic-analyses.html"><a href="allele-specific-transcriptomic-analyses.html#block-3"><i class="fa fa-check"></i><b>3.4.1</b> Block 3</a></li>
<li class="chapter" data-level="3.4.2" data-path="allele-specific-transcriptomic-analyses.html"><a href="allele-specific-transcriptomic-analyses.html#block-4"><i class="fa fa-check"></i><b>3.4.2</b> Block 4</a></li>
</ul></li>
</ul></li>
<li class="chapter" data-level="4" data-path="chip-seq-analysis.html"><a href="chip-seq-analysis.html"><i class="fa fa-check"></i><b>4</b> ChIP-seq Analysis</a>
<ul>
<li class="chapter" data-level="4.1" data-path="chip-seq-analysis.html"><a href="chip-seq-analysis.html#enrichment-across-promoters-and-gene-bodies"><i class="fa fa-check"></i><b>4.1</b> Enrichment across promoters and gene bodies</a></li>
<li class="chapter" data-level="4.2" data-path="chip-seq-analysis.html"><a href="chip-seq-analysis.html#differential-enrichment-analysis"><i class="fa fa-check"></i><b>4.2</b> Differential enrichment analysis</a>
<ul>
<li class="chapter" data-level="4.2.1" data-path="chip-seq-analysis.html"><a href="chip-seq-analysis.html#h3k27me3"><i class="fa fa-check"></i><b>4.2.1</b> H3K27me3</a></li>
<li class="chapter" data-level="4.2.2" data-path="chip-seq-analysis.html"><a href="chip-seq-analysis.html#h3k27ac"><i class="fa fa-check"></i><b>4.2.2</b> H3K27ac</a></li>
<li class="chapter" data-level="4.2.3" data-path="chip-seq-analysis.html"><a href="chip-seq-analysis.html#h3k4me3"><i class="fa fa-check"></i><b>4.2.3</b> H3K4me3</a></li>
</ul></li>
</ul></li>
<li class="chapter" data-level="5" data-path="allele-specific-chip-seq-analyses.html"><a href="allele-specific-chip-seq-analyses.html"><i class="fa fa-check"></i><b>5</b> Allele-Specific ChIP-seq Analyses</a>
<ul>
<li class="chapter" data-level="5.1" data-path="allele-specific-chip-seq-analyses.html"><a href="allele-specific-chip-seq-analyses.html#snps-and-peaks"><i class="fa fa-check"></i><b>5.1</b> SNPs and peaks</a></li>
<li class="chapter" data-level="5.2" data-path="allele-specific-chip-seq-analyses.html"><a href="allele-specific-chip-seq-analyses.html#poe-peak-lists"><i class="fa fa-check"></i><b>5.2</b> POE peak lists</a>
<ul>
<li class="chapter" data-level="5.2.1" data-path="allele-specific-chip-seq-analyses.html"><a href="allele-specific-chip-seq-analyses.html#h3k27me3-1"><i class="fa fa-check"></i><b>5.2.1</b> H3K27me3</a></li>
<li class="chapter" data-level="5.2.2" data-path="allele-specific-chip-seq-analyses.html"><a href="allele-specific-chip-seq-analyses.html#h3k27ac-1"><i class="fa fa-check"></i><b>5.2.2</b> H3K27ac</a></li>
<li class="chapter" data-level="5.2.3" data-path="allele-specific-chip-seq-analyses.html"><a href="allele-specific-chip-seq-analyses.html#h3k4me3-1"><i class="fa fa-check"></i><b>5.2.3</b> H3K4me3</a></li>
</ul></li>
<li class="chapter" data-level="5.3" data-path="allele-specific-chip-seq-analyses.html"><a href="allele-specific-chip-seq-analyses.html#h3k27me3-2"><i class="fa fa-check"></i><b>5.3</b> H3K27me3</a>
<ul>
<li class="chapter" data-level="5.3.1" data-path="allele-specific-chip-seq-analyses.html"><a href="allele-specific-chip-seq-analyses.html#gene-bodies"><i class="fa fa-check"></i><b>5.3.1</b> Gene bodies</a></li>
<li class="chapter" data-level="5.3.2" data-path="allele-specific-chip-seq-analyses.html"><a href="allele-specific-chip-seq-analyses.html#promoters"><i class="fa fa-check"></i><b>5.3.2</b> Promoters</a></li>
</ul></li>
<li class="chapter" data-level="5.4" data-path="allele-specific-chip-seq-analyses.html"><a href="allele-specific-chip-seq-analyses.html#h3k27ac-2"><i class="fa fa-check"></i><b>5.4</b> H3K27ac</a>
<ul>
<li class="chapter" data-level="5.4.1" data-path="allele-specific-chip-seq-analyses.html"><a href="allele-specific-chip-seq-analyses.html#gene-bodies-1"><i class="fa fa-check"></i><b>5.4.1</b> Gene bodies</a></li>
<li class="chapter" data-level="5.4.2" data-path="allele-specific-chip-seq-analyses.html"><a href="allele-specific-chip-seq-analyses.html#promoters-1"><i class="fa fa-check"></i><b>5.4.2</b> Promoters</a></li>
</ul></li>
<li class="chapter" data-level="5.5" data-path="allele-specific-chip-seq-analyses.html"><a href="allele-specific-chip-seq-analyses.html#h3k4me3-2"><i class="fa fa-check"></i><b>5.5</b> H3K4me3</a>
<ul>
<li class="chapter" data-level="5.5.1" data-path="allele-specific-chip-seq-analyses.html"><a href="allele-specific-chip-seq-analyses.html#gene-bodies-2"><i class="fa fa-check"></i><b>5.5.1</b> Gene bodies</a></li>
<li class="chapter" data-level="5.5.2" data-path="allele-specific-chip-seq-analyses.html"><a href="allele-specific-chip-seq-analyses.html#promoters-2"><i class="fa fa-check"></i><b>5.5.2</b> Promoters</a></li>
</ul></li>
<li class="chapter" data-level="5.6" data-path="allele-specific-chip-seq-analyses.html"><a href="allele-specific-chip-seq-analyses.html#combined-results"><i class="fa fa-check"></i><b>5.6</b> Combined results</a>
<ul>
<li class="chapter" data-level="5.6.1" data-path="allele-specific-chip-seq-analyses.html"><a href="allele-specific-chip-seq-analyses.html#block-1-7"><i class="fa fa-check"></i><b>5.6.1</b> Block 1</a></li>
<li class="chapter" data-level="5.6.2" data-path="allele-specific-chip-seq-analyses.html"><a href="allele-specific-chip-seq-analyses.html#block-2-7"><i class="fa fa-check"></i><b>5.6.2</b> Block 2</a></li>
</ul></li>
</ul></li>
<li class="chapter" data-level="6" data-path="hptm-transcription-dynamics.html"><a href="hptm-transcription-dynamics.html"><i class="fa fa-check"></i><b>6</b> HPTM-transcription dynamics</a>
<ul>
<li class="chapter" data-level="6.1" data-path="hptm-transcription-dynamics.html"><a href="hptm-transcription-dynamics.html#h3k27me3-3"><i class="fa fa-check"></i><b>6.1</b> H3K27me3</a>
<ul>
<li class="chapter" data-level="6.1.1" data-path="hptm-transcription-dynamics.html"><a href="hptm-transcription-dynamics.html#gene-bodies-3"><i class="fa fa-check"></i><b>6.1.1</b> Gene bodies</a></li>
<li class="chapter" data-level="6.1.2" data-path="hptm-transcription-dynamics.html"><a href="hptm-transcription-dynamics.html#promoters-3"><i class="fa fa-check"></i><b>6.1.2</b> Promoters</a></li>
</ul></li>
<li class="chapter" data-level="6.2" data-path="hptm-transcription-dynamics.html"><a href="hptm-transcription-dynamics.html#h3k27ac-3"><i class="fa fa-check"></i><b>6.2</b> H3K27ac</a>
<ul>
<li class="chapter" data-level="6.2.1" data-path="hptm-transcription-dynamics.html"><a href="hptm-transcription-dynamics.html#gene-bodies-4"><i class="fa fa-check"></i><b>6.2.1</b> Gene bodies</a></li>
<li class="chapter" data-level="6.2.2" data-path="hptm-transcription-dynamics.html"><a href="hptm-transcription-dynamics.html#promoters-4"><i class="fa fa-check"></i><b>6.2.2</b> Promoters</a></li>
</ul></li>
<li class="chapter" data-level="6.3" data-path="hptm-transcription-dynamics.html"><a href="hptm-transcription-dynamics.html#h3k4me3-3"><i class="fa fa-check"></i><b>6.3</b> H3K4me3</a>
<ul>
<li class="chapter" data-level="6.3.1" data-path="hptm-transcription-dynamics.html"><a href="hptm-transcription-dynamics.html#gene-bodies-5"><i class="fa fa-check"></i><b>6.3.1</b> Gene bodies</a></li>
<li class="chapter" data-level="6.3.2" data-path="hptm-transcription-dynamics.html"><a href="hptm-transcription-dynamics.html#promoters-5"><i class="fa fa-check"></i><b>6.3.2</b> Promoters</a></li>
</ul></li>
</ul></li>
<li class="chapter" data-level="7" data-path="poe-hptm-enrichment-poe-transcription-dynamics.html"><a href="poe-hptm-enrichment-poe-transcription-dynamics.html"><i class="fa fa-check"></i><b>7</b> POE HPTM enrichment-POE transcription dynamics</a>
<ul>
<li class="chapter" data-level="7.1" data-path="poe-hptm-enrichment-poe-transcription-dynamics.html"><a href="poe-hptm-enrichment-poe-transcription-dynamics.html#block-1-8"><i class="fa fa-check"></i><b>7.1</b> Block 1</a>
<ul>
<li class="chapter" data-level="" data-path="poe-hptm-enrichment-poe-transcription-dynamics.html"><a href="poe-hptm-enrichment-poe-transcription-dynamics.html#h3k27me3-4"><i class="fa fa-check"></i>H3K27me3</a></li>
<li class="chapter" data-level="" data-path="poe-hptm-enrichment-poe-transcription-dynamics.html"><a href="poe-hptm-enrichment-poe-transcription-dynamics.html#h3k27ac-4"><i class="fa fa-check"></i>H3K27ac</a></li>
<li class="chapter" data-level="" data-path="poe-hptm-enrichment-poe-transcription-dynamics.html"><a href="poe-hptm-enrichment-poe-transcription-dynamics.html#h3k4me3-4"><i class="fa fa-check"></i>H3K4me3</a></li>
</ul></li>
<li class="chapter" data-level="7.2" data-path="poe-hptm-enrichment-poe-transcription-dynamics.html"><a href="poe-hptm-enrichment-poe-transcription-dynamics.html#block-2-8"><i class="fa fa-check"></i><b>7.2</b> Block 2</a>
<ul>
<li class="chapter" data-level="" data-path="poe-hptm-enrichment-poe-transcription-dynamics.html"><a href="poe-hptm-enrichment-poe-transcription-dynamics.html#h3k27me3-5"><i class="fa fa-check"></i>H3K27me3</a></li>
<li class="chapter" data-level="" data-path="poe-hptm-enrichment-poe-transcription-dynamics.html"><a href="poe-hptm-enrichment-poe-transcription-dynamics.html#h3k27ac-5"><i class="fa fa-check"></i>H3K27ac</a></li>
<li class="chapter" data-level="" data-path="poe-hptm-enrichment-poe-transcription-dynamics.html"><a href="poe-hptm-enrichment-poe-transcription-dynamics.html#h3k4me3-5"><i class="fa fa-check"></i>H3K4me3</a></li>
</ul></li>
<li class="chapter" data-level="7.3" data-path="poe-hptm-enrichment-poe-transcription-dynamics.html"><a href="poe-hptm-enrichment-poe-transcription-dynamics.html#logistic-regression"><i class="fa fa-check"></i><b>7.3</b> Logistic regression</a>
<ul>
<li class="chapter" data-level="" data-path="poe-hptm-enrichment-poe-transcription-dynamics.html"><a href="poe-hptm-enrichment-poe-transcription-dynamics.html#h3k27me3-gene-body"><i class="fa fa-check"></i>H3K27me3 (gene body)</a></li>
<li class="chapter" data-level="" data-path="poe-hptm-enrichment-poe-transcription-dynamics.html"><a href="poe-hptm-enrichment-poe-transcription-dynamics.html#h3k27me3-promoter"><i class="fa fa-check"></i>H3K27me3 (promoter)</a></li>
<li class="chapter" data-level="" data-path="poe-hptm-enrichment-poe-transcription-dynamics.html"><a href="poe-hptm-enrichment-poe-transcription-dynamics.html#h3k27ac-gene-body"><i class="fa fa-check"></i>H3K27ac (gene body)</a></li>
<li class="chapter" data-level="" data-path="poe-hptm-enrichment-poe-transcription-dynamics.html"><a href="poe-hptm-enrichment-poe-transcription-dynamics.html#h3k27ac-promoter"><i class="fa fa-check"></i>H3K27ac (promoter)</a></li>
<li class="chapter" data-level="" data-path="poe-hptm-enrichment-poe-transcription-dynamics.html"><a href="poe-hptm-enrichment-poe-transcription-dynamics.html#h3k4me3-gene-body"><i class="fa fa-check"></i>H3K4me3 (gene body)</a></li>
<li class="chapter" data-level="" data-path="poe-hptm-enrichment-poe-transcription-dynamics.html"><a href="poe-hptm-enrichment-poe-transcription-dynamics.html#h3k4me3-promoter"><i class="fa fa-check"></i>H3K4me3 (promoter)</a></li>
</ul></li>
</ul></li>
<li class="chapter" data-level="8" data-path="go-enrichment-analyses.html"><a href="go-enrichment-analyses.html"><i class="fa fa-check"></i><b>8</b> GO enrichment analyses</a>
<ul>
<li class="chapter" data-level="8.1" data-path="go-enrichment-analyses.html"><a href="go-enrichment-analyses.html#degs-poe-genes"><i class="fa fa-check"></i><b>8.1</b> DEGs & POE genes</a></li>
<li class="chapter" data-level="8.2" data-path="go-enrichment-analyses.html"><a href="go-enrichment-analyses.html#wgcna-modules"><i class="fa fa-check"></i><b>8.2</b> WGCNA modules</a></li>
<li class="chapter" data-level="8.3" data-path="go-enrichment-analyses.html"><a href="go-enrichment-analyses.html#hptm-differentially-enriched-regions"><i class="fa fa-check"></i><b>8.3</b> HPTM differentially enriched regions</a></li>
</ul></li>
<li class="chapter" data-level="9" data-path="poe-gene-feature-assessment.html"><a href="poe-gene-feature-assessment.html"><i class="fa fa-check"></i><b>9</b> POE gene feature assessment</a>
<ul>
<li class="chapter" data-level="9.1" data-path="poe-gene-feature-assessment.html"><a href="poe-gene-feature-assessment.html#spatial-clustering"><i class="fa fa-check"></i><b>9.1</b> Spatial clustering</a></li>
<li class="chapter" data-level="9.2" data-path="poe-gene-feature-assessment.html"><a href="poe-gene-feature-assessment.html#intron-feature-analyses"><i class="fa fa-check"></i><b>9.2</b> Intron feature analyses</a>
<ul>
<li class="chapter" data-level="" data-path="poe-gene-feature-assessment.html"><a href="poe-gene-feature-assessment.html#recombination-rate"><i class="fa fa-check"></i>Recombination rate</a></li>
<li class="chapter" data-level="" data-path="poe-gene-feature-assessment.html"><a href="poe-gene-feature-assessment.html#intron"><i class="fa fa-check"></i>% intron</a></li>
<li class="chapter" data-level="" data-path="poe-gene-feature-assessment.html"><a href="poe-gene-feature-assessment.html#intron-gc"><i class="fa fa-check"></i>Intron GC</a></li>
<li class="chapter" data-level="" data-path="poe-gene-feature-assessment.html"><a href="poe-gene-feature-assessment.html#intron-cpg-density"><i class="fa fa-check"></i>Intron CpG density</a></li>
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<div id="poe-hptm-enrichment-poe-transcription-dynamics" class="section level1 hasAnchor" number="7">
<h1><span class="header-section-number">S7</span> POE HPTM enrichment-POE transcription dynamics<a href="poe-hptm-enrichment-poe-transcription-dynamics.html#poe-hptm-enrichment-poe-transcription-dynamics" class="anchor-section" aria-label="Anchor link to header"></a></h1>
<div id="block-1-8" class="section level2 hasAnchor" number="7.1">
<h2><span class="header-section-number">7.1</span> Block 1<a href="poe-hptm-enrichment-poe-transcription-dynamics.html#block-1-8" class="anchor-section" aria-label="Anchor link to header"></a></h2>
<div id="h3k27me3-4" class="section level3 unnumbered hasAnchor">
<h3>H3K27me3<a href="poe-hptm-enrichment-poe-transcription-dynamics.html#h3k27me3-4" class="anchor-section" aria-label="Anchor link to header"></a></h3>
<div id="gene-body" class="section level4 unnumbered hasAnchor">
<h4>Gene body<a href="poe-hptm-enrichment-poe-transcription-dynamics.html#gene-body" class="anchor-section" aria-label="Anchor link to header"></a></h4>
<div id="wl" class="section level5 unnumbered hasAnchor">
<h5>WL<a href="poe-hptm-enrichment-poe-transcription-dynamics.html#wl" class="anchor-section" aria-label="Anchor link to header"></a></h5>
<p>Gene:Peak (categories of allelic bias)</p>
<pre><code>##
## Lineage A:Lineage A Lineage A:NA Lineage A:pat Lineage B:Lineage A
## 1 4 1 11
## Lineage B:Lineage B Lineage B:mat Lineage B:NA Lineage B:pat
## 2 7 40 5
## mat:Lineage A mat:Lineage B mat:mat mat:NA
## 7 1 9 20
## mat:pat NA:Lineage A NA:Lineage B NA:mat
## 11 1215 322 1541
## NA:NA NA:pat pat:Lineage A pat:Lineage B
## 6981 2639 36 5
## pat:mat pat:NA pat:pat
## 59 229 105</code></pre>
<p>Summary of POE overlaps (00 = neither peak nor gene biased, 01 = gene unbiased, peak biased, 10 = gene biased, peak unbiased, 11 = both gene and peak show allelic bias)</p>
<pre><code>##
## 00 01 10 11
## 12234 25 259 184</code></pre>
<p>Fishers exact test of enrichment (do genes showing allelic bias overlap with peaks showing allelic bias)?</p>
<pre><code>##
## Fisher's Exact Test for Count Data
##
## data: data.frame(x = c(tab[4], tab[3]), y = c(tab[2], tab[1]))
## p-value < 2.2e-16
## alternative hypothesis: true odds ratio is greater than 1
## 95 percent confidence interval:
## 236.9345 Inf
## sample estimates:
## odds ratio
## 347.5206</code></pre>
<p>ASI: “allelic similarlty index”. Here, the axis values represent allelic transcription (x) and HPTM enrichment (y), with positive values being biased toward the paternal allele, and negative values being biased toward the maternal allele. ASI values are “=” for transcript and peak being baised toward the same allele, “NS” for either transcript or peak not showing allelic bias, and “≠” for biased toward opposite alleles.</p>
<p><img src="bookdownproj_files/figure-html/unnamed-chunk-13-1.png" width="672" /></p>
</div>
<div id="ql" class="section level5 unnumbered hasAnchor">
<h5>QL<a href="poe-hptm-enrichment-poe-transcription-dynamics.html#ql" class="anchor-section" aria-label="Anchor link to header"></a></h5>
<p>Gene:Peak (categories of allelic bias)</p>
<pre><code>##
## Lineage A:Lineage A Lineage A:NA Lineage A:pat Lineage B:Lineage A
## 2 2 2 1
## Lineage B:mat Lineage B:NA Lineage B:pat mat:Lineage A
## 1 12 17 3
## mat:Lineage B mat:mat mat:NA mat:pat
## 1 2 50 31
## NA:Lineage A NA:Lineage B NA:mat NA:NA
## 759 338 1534 9161
## NA:pat pat:Lineage A pat:Lineage B pat:mat
## 5776 33 16 49
## pat:NA pat:pat
## 324 231</code></pre>
<p>Summary of overlaps (00 = neither peak nor gene biased, 01 = gene unbiased, peak biased, 10 = gene biased, peak unbiased, 11 = both gene and peak show allelic bias)</p>
<pre><code>##
## 00 01 10 11
## 16843 55 366 313</code></pre>
<p>Fishers exact test of enrichment (do genes showing allelic bias overlap with peaks showing allelic bias)?</p>
<pre><code>##
## Fisher's Exact Test for Count Data
##
## data: data.frame(x = c(tab[4], tab[3]), y = c(tab[2], tab[1]))
## p-value < 2.2e-16
## alternative hypothesis: true odds ratio is greater than 1
## 95 percent confidence interval:
## 199.8675 Inf
## sample estimates:
## odds ratio
## 260.0518</code></pre>
<p><img src="bookdownproj_files/figure-html/unnamed-chunk-18-1.png" width="672" /></p>
</div>
</div>
<div id="promoter" class="section level4 unnumbered hasAnchor">
<h4>Promoter<a href="poe-hptm-enrichment-poe-transcription-dynamics.html#promoter" class="anchor-section" aria-label="Anchor link to header"></a></h4>
<div id="wl-1" class="section level5 unnumbered hasAnchor">
<h5>WL<a href="poe-hptm-enrichment-poe-transcription-dynamics.html#wl-1" class="anchor-section" aria-label="Anchor link to header"></a></h5>
<p>Gene:Peak (categories of allelic bias)</p>
<pre><code>##
## Lineage A:Lineage A Lineage A:NA Lineage B:NA mat:mat
## 1 1 3 2
## mat:NA mat:pat NA:Lineage A NA:Lineage B
## 3 2 178 39
## NA:mat NA:NA NA:pat pat:Lineage A
## 217 1008 371 5
## pat:mat pat:NA pat:pat
## 8 31 18</code></pre>
<p>Summary of overlaps (00 = neither peak nor gene biased, 01 = gene unbiased, peak biased, 10 = gene biased, peak unbiased, 11 = both gene and peak show allelic bias)</p>
<pre><code>##
## 00 01 10 11
## 1775 3 5 30</code></pre>
<p>Fishers exact test of enrichment (do genes showing allelic bias overlap with peaks showing allelic bias)?</p>
<pre><code>##
## Fisher's Exact Test for Count Data
##
## data: data.frame(x = c(tab[4], tab[3]), y = c(tab[2], tab[1]))
## p-value < 2.2e-16
## alternative hypothesis: true odds ratio is greater than 1
## 95 percent confidence interval:
## 837.0586 Inf
## sample estimates:
## odds ratio
## 3190.375</code></pre>
<p><img src="bookdownproj_files/figure-html/unnamed-chunk-24-1.png" width="672" /></p>
</div>
<div id="ql-1" class="section level5 unnumbered hasAnchor">
<h5>QL<a href="poe-hptm-enrichment-poe-transcription-dynamics.html#ql-1" class="anchor-section" aria-label="Anchor link to header"></a></h5>
<p>Gene:Peak (categories of allelic bias)</p>
<pre><code>##
## Lineage A:NA Lineage A:pat Lineage B:NA mat:Lineage B mat:NA
## 2 2 2 1 2
## mat:pat NA:Lineage A NA:Lineage B NA:mat NA:NA
## 2 118 37 187 1164
## NA:pat pat:Lineage A pat:mat pat:NA pat:pat
## 899 8 10 38 34</code></pre>
<p>Summary of overlaps (00 = neither peak nor gene biased, 01 = gene unbiased, peak biased, 10 = gene biased, peak unbiased, 11 = both gene and peak show allelic bias)</p>
<pre><code>##
## 00 01 10 11
## 2341 11 12 46</code></pre>
<p>Fishers exact test of enrichment (do genes showing allelic bias overlap with peaks showing allelic bias)?</p>
<pre><code>##
## Fisher's Exact Test for Count Data
##
## data: data.frame(x = c(tab[4], tab[3]), y = c(tab[2], tab[1]))
## p-value < 2.2e-16
## alternative hypothesis: true odds ratio is greater than 1
## 95 percent confidence interval:
## 358.0999 Inf
## sample estimates:
## odds ratio
## 798.7605</code></pre>
<p><img src="bookdownproj_files/figure-html/unnamed-chunk-29-1.png" width="672" /></p>
</div>
</div>
</div>
<div id="h3k27ac-4" class="section level3 unnumbered hasAnchor">
<h3>H3K27ac<a href="poe-hptm-enrichment-poe-transcription-dynamics.html#h3k27ac-4" class="anchor-section" aria-label="Anchor link to header"></a></h3>
<div id="gene-body-1" class="section level4 unnumbered hasAnchor">
<h4>Gene body<a href="poe-hptm-enrichment-poe-transcription-dynamics.html#gene-body-1" class="anchor-section" aria-label="Anchor link to header"></a></h4>
<div id="wl-2" class="section level5 unnumbered hasAnchor">
<h5>WL<a href="poe-hptm-enrichment-poe-transcription-dynamics.html#wl-2" class="anchor-section" aria-label="Anchor link to header"></a></h5>
<p>Gene:Peak (categories of allelic bias)</p>
<pre><code>##
## Lineage A:Lineage A Lineage A:NA Lineage A:pat Lineage B:Lineage A
## 2 7 1 7
## Lineage B:Lineage B Lineage B:mat Lineage B:NA Lineage B:pat
## 1 16 41 11
## mat:Lineage A mat:Lineage B mat:mat mat:NA
## 3 1 2 27
## mat:pat NA:Lineage A NA:Lineage B NA:mat
## 16 1086 247 1864
## NA:NA NA:pat pat:Lineage A pat:Lineage B
## 7627 2986 32 10
## pat:mat pat:NA pat:pat
## 63 233 120</code></pre>
<p>Summary of overlaps (00 = neither peak nor gene biased, 01 = gene unbiased, peak biased, 10 = gene biased, peak unbiased, 11 = both gene and peak show allelic bias)</p>
<pre><code>##
## 00 01 10 11
## 13326 32 253 201</code></pre>
<p>Fishers exact test of enrichment (do genes showing allelic bias overlap with peaks showing allelic bias)?</p>
<pre><code>##
## Fisher's Exact Test for Count Data
##
## data: data.frame(x = c(tab[4], tab[3]), y = c(tab[2], tab[1]))
## p-value < 2.2e-16
## alternative hypothesis: true odds ratio is greater than 1
## 95 percent confidence interval:
## 233.7337 Inf
## sample estimates:
## odds ratio
## 332.4454</code></pre>
<p><img src="bookdownproj_files/figure-html/unnamed-chunk-38-1.png" width="672" /></p>
</div>
<div id="ql-2" class="section level5 unnumbered hasAnchor">
<h5>QL<a href="poe-hptm-enrichment-poe-transcription-dynamics.html#ql-2" class="anchor-section" aria-label="Anchor link to header"></a></h5>
<p>Gene:Peak (categories of allelic bias)</p>
<pre><code>##
## Lineage A:NA Lineage A:pat Lineage B:Lineage A Lineage B:Lineage B
## 2 5 1 1
## Lineage B:mat Lineage B:NA Lineage B:pat mat:Lineage A
## 1 18 16 5
## mat:Lineage B mat:mat mat:NA mat:pat
## 1 1 39 19
## NA:Lineage A NA:Lineage B NA:mat NA:NA
## 919 430 1333 8827
## NA:pat pat:Lineage A pat:Lineage B pat:mat
## 5847 31 24 48
## pat:NA pat:pat
## 320 250</code></pre>
<p>Summary of overlaps (00 = neither peak nor gene biased, 01 = gene unbiased, peak biased, 10 = gene biased, peak unbiased, 11 = both gene and peak show allelic bias)</p>
<pre><code>##
## 00 01 10 11
## 16609 69 366 318</code></pre>
<p>Fishers exact test of enrichment (do genes showing allelic bias overlap with peaks showing allelic bias)?</p>
<pre><code>##
## Fisher's Exact Test for Count Data
##
## data: data.frame(x = c(tab[4], tab[3]), y = c(tab[2], tab[1]))
## p-value < 2.2e-16
## alternative hypothesis: true odds ratio is greater than 1
## 95 percent confidence interval:
## 164.6826 Inf
## sample estimates:
## odds ratio
## 208.1453</code></pre>
<p><img src="bookdownproj_files/figure-html/unnamed-chunk-43-1.png" width="672" /></p>
</div>
</div>
<div id="promoter-1" class="section level4 unnumbered hasAnchor">
<h4>Promoter<a href="poe-hptm-enrichment-poe-transcription-dynamics.html#promoter-1" class="anchor-section" aria-label="Anchor link to header"></a></h4>
<div id="wl-3" class="section level5 unnumbered hasAnchor">
<h5>WL<a href="poe-hptm-enrichment-poe-transcription-dynamics.html#wl-3" class="anchor-section" aria-label="Anchor link to header"></a></h5>
<p>Gene:Peak (categories of allelic bias)</p>
<pre><code>##
## Lineage A:Lineage A Lineage A:NA Lineage B:NA Lineage B:pat
## 1 1 3 2
## mat:mat mat:NA mat:pat NA:Lineage A
## 2 3 1 180
## NA:Lineage B NA:mat NA:NA NA:pat
## 38 265 1256 482
## pat:Lineage A pat:Lineage B pat:mat pat:NA
## 3 3 9 40
## pat:pat
## 20</code></pre>
<p>Summary of overlaps (00 = neither peak nor gene biased, 01 = gene unbiased, peak biased, 10 = gene biased, peak unbiased, 11 = both gene and peak show allelic bias)</p>
<pre><code>##
## 00 01 10 11
## 2176 7 7 32</code></pre>
<p>Fishers exact test of enrichment (do genes showing allelic bias overlap with peaks showing allelic bias)?</p>
<pre><code>##
## Fisher's Exact Test for Count Data
##
## data: data.frame(x = c(tab[4], tab[3]), y = c(tab[2], tab[1]))
## p-value < 2.2e-16
## alternative hypothesis: true odds ratio is greater than 1
## 95 percent confidence interval:
## 488.4372 Inf
## sample estimates:
## odds ratio
## 1342.753</code></pre>
<p><img src="bookdownproj_files/figure-html/unnamed-chunk-49-1.png" width="672" /></p>
</div>
<div id="ql-3" class="section level5 unnumbered hasAnchor">
<h5>QL<a href="poe-hptm-enrichment-poe-transcription-dynamics.html#ql-3" class="anchor-section" aria-label="Anchor link to header"></a></h5>
<p>Gene:Peak (categories of allelic bias)</p>
<pre><code>##
## Lineage A:NA Lineage A:pat Lineage B:NA Lineage B:pat mat:Lineage B
## 1 3 1 1 1
## mat:NA mat:pat NA:Lineage A NA:Lineage B NA:mat
## 2 1 113 56 192
## NA:NA NA:pat pat:Lineage A pat:Lineage B pat:mat
## 1219 859 2 2 6
## pat:NA pat:pat
## 42 33</code></pre>
<p>Summary of overlaps (00 = neither peak nor gene biased, 01 = gene unbiased, peak biased, 10 = gene biased, peak unbiased, 11 = both gene and peak show allelic bias)</p>
<pre><code>##
## 00 01 10 11
## 2380 11 12 40</code></pre>
<p>Fishers exact test of enrichment (do genes showing allelic bias overlap with peaks showing allelic bias)?</p>
<pre><code>##
## Fisher's Exact Test for Count Data
##
## data: data.frame(x = c(tab[4], tab[3]), y = c(tab[2], tab[1]))
## p-value < 2.2e-16
## alternative hypothesis: true odds ratio is greater than 1
## 95 percent confidence interval:
## 313.8559 Inf
## sample estimates:
## odds ratio
## 700.1813</code></pre>
<p><img src="bookdownproj_files/figure-html/unnamed-chunk-55-1.png" width="672" /></p>
</div>
</div>
</div>
<div id="h3k4me3-4" class="section level3 unnumbered hasAnchor">
<h3>H3K4me3<a href="poe-hptm-enrichment-poe-transcription-dynamics.html#h3k4me3-4" class="anchor-section" aria-label="Anchor link to header"></a></h3>
<div id="gene-body-2" class="section level4 unnumbered hasAnchor">
<h4>Gene body<a href="poe-hptm-enrichment-poe-transcription-dynamics.html#gene-body-2" class="anchor-section" aria-label="Anchor link to header"></a></h4>
<div id="wl-4" class="section level5 unnumbered hasAnchor">
<h5>WL<a href="poe-hptm-enrichment-poe-transcription-dynamics.html#wl-4" class="anchor-section" aria-label="Anchor link to header"></a></h5>
<p>Gene:Peak (categories of allelic bias)</p>
<pre><code>##
## Lineage A:Lineage A Lineage A:NA Lineage A:pat Lineage B:Lineage A
## 2 5 4 3
## Lineage B:Lineage B Lineage B:mat Lineage B:NA Lineage B:pat
## 1 13 32 9
## mat:Lineage A mat:mat mat:NA mat:pat
## 2 6 21 12
## NA:Lineage A NA:Lineage B NA:mat NA:NA
## 539 128 1786 7420
## NA:pat pat:Lineage A pat:Lineage B pat:mat
## 2843 14 6 48
## pat:NA pat:pat
## 213 110</code></pre>
<p>Summary of overlaps (00 = neither peak nor gene biased, 01 = gene unbiased, peak biased, 10 = gene biased, peak unbiased, 11 = both gene and peak show allelic bias)</p>
<pre><code>##
## 00 01 10 11
## 12322 14 208 176</code></pre>
<p>Fishers exact test of enrichment (do genes showing allelic bias overlap with peaks showing allelic bias)?</p>
<pre><code>##
## Fisher's Exact Test for Count Data
##
## data: data.frame(x = c(tab[4], tab[3]), y = c(tab[2], tab[1]))
## p-value < 2.2e-16
## alternative hypothesis: true odds ratio is greater than 1
## 95 percent confidence interval:
## 459.8188 Inf
## sample estimates:
## odds ratio
## 741.8472</code></pre>
<p><img src="bookdownproj_files/figure-html/unnamed-chunk-63-1.png" width="672" /></p>
</div>
<div id="ql-4" class="section level5 unnumbered hasAnchor">
<h5>QL<a href="poe-hptm-enrichment-poe-transcription-dynamics.html#ql-4" class="anchor-section" aria-label="Anchor link to header"></a></h5>
<p>Gene:Peak (categories of allelic bias)</p>
<pre><code>##
## Lineage A:Lineage A Lineage A:NA Lineage A:pat Lineage B:Lineage B
## 1 3 4 1
## Lineage B:mat Lineage B:NA Lineage B:pat mat:Lineage A
## 2 15 9 5
## mat:Lineage B mat:mat mat:NA mat:pat
## 1 4 28 26
## NA:Lineage A NA:Lineage B NA:mat NA:NA
## 609 272 1237 8025
## NA:pat pat:Lineage A pat:Lineage B pat:mat
## 4844 25 22 43
## pat:NA pat:pat
## 297 224</code></pre>
<p>Summary of overlaps (00 = neither peak nor gene biased, 01 = gene unbiased, peak biased, 10 = gene biased, peak unbiased, 11 = both gene and peak show allelic bias)</p>
<pre><code>##
## 00 01 10 11
## 14332 41 329 297</code></pre>
<p>Fishers exact test of enrichment (do genes showing allelic bias overlap with peaks showing allelic bias)?</p>
<pre><code>##
## Fisher's Exact Test for Count Data
##
## data: data.frame(x = c(tab[4], tab[3]), y = c(tab[2], tab[1]))
## p-value < 2.2e-16
## alternative hypothesis: true odds ratio is greater than 1
## 95 percent confidence interval:
## 235.3106 Inf
## sample estimates:
## odds ratio
## 315.9013</code></pre>
<p><img src="bookdownproj_files/figure-html/unnamed-chunk-68-1.png" width="672" /></p>
</div>
</div>
<div id="promoter-2" class="section level4 unnumbered hasAnchor">
<h4>Promoter<a href="poe-hptm-enrichment-poe-transcription-dynamics.html#promoter-2" class="anchor-section" aria-label="Anchor link to header"></a></h4>
<div id="wl-5" class="section level5 unnumbered hasAnchor">
<h5>WL<a href="poe-hptm-enrichment-poe-transcription-dynamics.html#wl-5" class="anchor-section" aria-label="Anchor link to header"></a></h5>
<p>Gene:Peak (categories of allelic bias)</p>
<pre><code>##
## Lineage A:Lineage A Lineage A:NA Lineage A:pat Lineage B:NA
## 1 1 1 1
## Lineage B:pat mat:mat mat:NA mat:pat
## 3 1 2 1
## NA:Lineage A NA:Lineage B NA:mat NA:NA
## 94 17 267 1104
## NA:pat pat:Lineage A pat:Lineage B pat:mat
## 465 3 1 8
## pat:NA pat:pat
## 33 26</code></pre>
<p>Summary of overlaps (00 = neither peak nor gene biased, 01 = gene unbiased, peak biased, 10 = gene biased, peak unbiased, 11 = both gene and peak show allelic bias)</p>
<pre><code>##
## 00 01 10 11
## 1907 3 3 36</code></pre>
<p>Fishers exact test of enrichment (do genes showing allelic bias overlap with peaks showing allelic bias)?</p>
<pre><code>##
## Fisher's Exact Test for Count Data
##
## data: data.frame(x = c(tab[4], tab[3]), y = c(tab[2], tab[1]))
## p-value < 2.2e-16
## alternative hypothesis: true odds ratio is greater than 1
## 95 percent confidence interval:
## 1602.424 Inf
## sample estimates:
## odds ratio
## 7569.223</code></pre>
<p><img src="bookdownproj_files/figure-html/unnamed-chunk-74-1.png" width="672" /></p>
</div>
<div id="ql-5" class="section level5 unnumbered hasAnchor">
<h5>QL<a href="poe-hptm-enrichment-poe-transcription-dynamics.html#ql-5" class="anchor-section" aria-label="Anchor link to header"></a></h5>
<p>Gene:Peak (categories of allelic bias)</p>
<pre><code>##
## Lineage A:NA Lineage A:pat Lineage B:pat mat:Lineage B mat:mat
## 3 3 2 1 2
## mat:NA NA:Lineage A NA:Lineage B NA:mat NA:NA
## 2 74 36 167 1075
## NA:pat pat:Lineage A pat:Lineage B pat:mat pat:NA
## 697 1 3 3 44
## pat:pat
## 35</code></pre>
<p>Summary of overlaps (00 = neither peak nor gene biased, 01 = gene unbiased, peak biased, 10 = gene biased, peak unbiased, 11 = both gene and peak show allelic bias)</p>
<pre><code>##
## 00 01 10 11
## 1998 6 9 40</code></pre>
<p>Fishers exact test of enrichment (do genes showing allelic bias overlap with peaks showing allelic bias)?</p>
<pre><code>##
## Fisher's Exact Test for Count Data
##
## data: data.frame(x = c(tab[4], tab[3]), y = c(tab[2], tab[1]))
## p-value < 2.2e-16
## alternative hypothesis: true odds ratio is greater than 1
## 95 percent confidence interval:
## 521.7834 Inf
## sample estimates:
## odds ratio
## 1346.678</code></pre>
<p><img src="bookdownproj_files/figure-html/unnamed-chunk-80-1.png" width="672" /></p>
</div>
</div>
</div>
</div>
<div id="block-2-8" class="section level2 hasAnchor" number="7.2">
<h2><span class="header-section-number">7.2</span> Block 2<a href="poe-hptm-enrichment-poe-transcription-dynamics.html#block-2-8" class="anchor-section" aria-label="Anchor link to header"></a></h2>
<div id="h3k27me3-5" class="section level3 unnumbered hasAnchor">
<h3>H3K27me3<a href="poe-hptm-enrichment-poe-transcription-dynamics.html#h3k27me3-5" class="anchor-section" aria-label="Anchor link to header"></a></h3>
<div id="gene-body-3" class="section level4 unnumbered hasAnchor">
<h4>Gene body<a href="poe-hptm-enrichment-poe-transcription-dynamics.html#gene-body-3" class="anchor-section" aria-label="Anchor link to header"></a></h4>
<div id="wl-6" class="section level5 unnumbered hasAnchor">
<h5>WL<a href="poe-hptm-enrichment-poe-transcription-dynamics.html#wl-6" class="anchor-section" aria-label="Anchor link to header"></a></h5>
<p>Gene:Peak (categories of allelic bias)</p>
<pre><code>##
## Lineage B:Lineage A Lineage B:mat Lineage B:NA Lineage B:pat
## 1 1 11 3
## mat:Lineage A mat:Lineage B mat:mat mat:NA
## 4 3 19 54
## mat:pat NA:Lineage A NA:Lineage B NA:mat
## 10 569 727 1436
## NA:NA NA:pat pat:Lineage A pat:Lineage B
## 5053 1949 6 17
## pat:mat pat:NA pat:pat
## 37 83 29</code></pre>
<p>Summary of overlaps (00 = neither peak nor gene biased, 01 = gene unbiased, peak biased, 10 = gene biased, peak unbiased, 11 = both gene and peak show allelic bias)</p>
<pre><code>##
## 00 01 10 11
## 9474 23 145 95</code></pre>
<p>Fishers exact test of enrichment (do genes showing allelic bias overlap with peaks showing allelic bias)?</p>
<pre><code>##
## Fisher's Exact Test for Count Data
##
## data: data.frame(x = c(tab[4], tab[3]), y = c(tab[2], tab[1]))
## p-value < 2.2e-16
## alternative hypothesis: true odds ratio is greater than 1
## 95 percent confidence interval:
## 175.8221 Inf
## sample estimates:
## odds ratio
## 269.862</code></pre>
<p><img src="bookdownproj_files/figure-html/unnamed-chunk-89-1.png" width="672" /></p>
</div>
<div id="ql-6" class="section level5 unnumbered hasAnchor">
<h5>QL<a href="poe-hptm-enrichment-poe-transcription-dynamics.html#ql-6" class="anchor-section" aria-label="Anchor link to header"></a></h5>
<p>Gene:Peak (categories of allelic bias)</p>
<pre><code>##
## Lineage B:Lineage A Lineage B:Lineage B Lineage B:mat Lineage B:NA
## 1 2 3 7
## Lineage B:pat mat:Lineage A mat:Lineage B mat:mat
## 6 1 1 1
## mat:NA mat:pat NA:Lineage A NA:Lineage B
## 15 6 563 617
## NA:mat NA:NA NA:pat pat:Lineage A
## 941 5414 3362 3
## pat:Lineage B pat:mat pat:NA pat:pat
## 8 10 84 73</code></pre>
<p>Summary of overlaps (00 = neither peak nor gene biased, 01 = gene unbiased, peak biased, 10 = gene biased, peak unbiased, 11 = both gene and peak show allelic bias)</p>
<pre><code>##
## 00 01 10 11
## 10691 26 98 90</code></pre>
<p>Fishers exact test of enrichment (do genes showing allelic bias overlap with peaks showing allelic bias)?</p>
<pre><code>##
## Fisher's Exact Test for Count Data
##
## data: data.frame(x = c(tab[4], tab[3]), y = c(tab[2], tab[1]))
## p-value < 2.2e-16
## alternative hypothesis: true odds ratio is greater than 1
## 95 percent confidence interval:
## 245.3571 Inf
## sample estimates:
## odds ratio
## 374.0261</code></pre>
<p><img src="bookdownproj_files/figure-html/unnamed-chunk-94-1.png" width="672" /></p>
</div>
</div>
<div id="promoter-3" class="section level4 unnumbered hasAnchor">
<h4>Promoter<a href="poe-hptm-enrichment-poe-transcription-dynamics.html#promoter-3" class="anchor-section" aria-label="Anchor link to header"></a></h4>
<div id="wl-7" class="section level5 unnumbered hasAnchor">
<h5>WL<a href="poe-hptm-enrichment-poe-transcription-dynamics.html#wl-7" class="anchor-section" aria-label="Anchor link to header"></a></h5>
<p>Gene:Peak (categories of allelic bias)</p>
<pre><code>##
## mat:mat mat:NA mat:pat NA:Lineage A NA:Lineage B
## 1 9 1 72 79
## NA:mat NA:NA NA:pat pat:Lineage A pat:Lineage B
## 220 763 249 1 1
## pat:mat pat:NA pat:pat
## 2 11 3</code></pre>
<p>Summary of overlaps (00 = neither peak nor gene biased, 01 = gene unbiased, peak biased, 10 = gene biased, peak unbiased, 11 = both gene and peak show allelic bias)</p>
<pre><code>##
## 00 01 11
## 1376 3 7</code></pre>
<p>Fishers exact test of enrichment (do genes showing allelic bias overlap with peaks showing allelic bias)?</p>
<pre><code>## [1] "NA"</code></pre>
<p><img src="bookdownproj_files/figure-html/unnamed-chunk-100-1.png" width="672" /></p>
</div>
<div id="ql-7" class="section level5 unnumbered hasAnchor">
<h5>QL<a href="poe-hptm-enrichment-poe-transcription-dynamics.html#ql-7" class="anchor-section" aria-label="Anchor link to header"></a></h5>
<p>Gene:Peak (categories of allelic bias)</p>
<pre><code>##
## Lineage B:NA Lineage B:pat mat:NA mat:pat NA:Lineage A
## 1 1 3 3 86
## NA:Lineage B NA:mat NA:NA NA:pat pat:Lineage A
## 99 129 865 561 1
## pat:Lineage B pat:NA pat:pat
## 3 20 16</code></pre>
<p>Summary of overlaps (00 = neither peak nor gene biased, 01 = gene unbiased, peak biased, 10 = gene biased, peak unbiased, 11 = both gene and peak show allelic bias)</p>
<pre><code>##
## 00 01 10 11
## 1720 2 4 19</code></pre>
<p>Fishers exact test of enrichment (do genes showing allelic bias overlap with peaks showing allelic bias)?</p>
<pre><code>##
## Fisher's Exact Test for Count Data
##
## data: data.frame(x = c(tab[4], tab[3]), y = c(tab[2], tab[1]))
## p-value < 2.2e-16
## alternative hypothesis: true odds ratio is greater than 1
## 95 percent confidence interval:
## 721.7098 Inf
## sample estimates:
## odds ratio
## 3533.803</code></pre>
<p><img src="bookdownproj_files/figure-html/unnamed-chunk-106-1.png" width="672" /></p>
</div>
</div>
</div>
<div id="h3k27ac-5" class="section level3 unnumbered hasAnchor">
<h3>H3K27ac<a href="poe-hptm-enrichment-poe-transcription-dynamics.html#h3k27ac-5" class="anchor-section" aria-label="Anchor link to header"></a></h3>
<div id="gene-body-4" class="section level4 unnumbered hasAnchor">
<h4>Gene body<a href="poe-hptm-enrichment-poe-transcription-dynamics.html#gene-body-4" class="anchor-section" aria-label="Anchor link to header"></a></h4>
<div id="wl-8" class="section level5 unnumbered hasAnchor">
<h5>WL<a href="poe-hptm-enrichment-poe-transcription-dynamics.html#wl-8" class="anchor-section" aria-label="Anchor link to header"></a></h5>
<p>Gene:Peak (categories of allelic bias)</p>
<pre><code>##
## Lineage B:Lineage A Lineage B:mat Lineage B:NA Lineage B:pat
## 1 2 6 3
## mat:Lineage A mat:Lineage B mat:mat mat:NA
## 3 6 10 41
## mat:pat NA:Lineage A NA:Lineage B NA:mat
## 9 282 336 843
## NA:NA NA:pat pat:Lineage A pat:Lineage B
## 2933 1191 2 9
## pat:mat pat:NA pat:pat
## 24 40 28</code></pre>
<p>Summary of overlaps (00 = neither peak nor gene biased, 01 = gene unbiased, peak biased, 10 = gene biased, peak unbiased, 11 = both gene and peak show allelic bias)</p>
<pre><code>##
## 00 01 10 11
## 5415 16 85 71</code></pre>
<p>Fishers exact test of enrichment (do genes showing allelic bias overlap with peaks showing allelic bias)?</p>
<pre><code>##
## Fisher's Exact Test for Count Data
##
## data: data.frame(x = c(tab[4], tab[3]), y = c(tab[2], tab[1]))
## p-value < 2.2e-16
## alternative hypothesis: true odds ratio is greater than 1
## 95 percent confidence interval:
## 167.0016 Inf
## sample estimates:
## odds ratio
## 281.5192</code></pre>
<p><img src="bookdownproj_files/figure-html/unnamed-chunk-114-1.png" width="672" /></p>
</div>
<div id="ql-8" class="section level5 unnumbered hasAnchor">
<h5>QL<a href="poe-hptm-enrichment-poe-transcription-dynamics.html#ql-8" class="anchor-section" aria-label="Anchor link to header"></a></h5>
<p>Gene:Peak (categories of allelic bias)</p>
<pre><code>##
## Lineage B:Lineage A Lineage B:mat Lineage B:NA Lineage B:pat
## 6 2 17 5
## mat:Lineage A mat:Lineage B mat:mat mat:NA
## 3 2 2 25
## mat:pat NA:Lineage A NA:Lineage B NA:mat
## 17 605 613 950
## NA:NA NA:pat pat:Lineage A pat:Lineage B
## 5427 3388 8 5
## pat:mat pat:NA pat:pat
## 8 64 84</code></pre>
<p>Summary of overlaps (00 = neither peak nor gene biased, 01 = gene unbiased, peak biased, 10 = gene biased, peak unbiased, 11 = both gene and peak show allelic bias)</p>
<pre><code>##
## 00 01 10 11
## 10757 32 93 111</code></pre>
<p>Fishers exact test of enrichment (do genes showing allelic bias overlap with peaks showing allelic bias)?</p>
<pre><code>##
## Fisher's Exact Test for Count Data
##
## data: data.frame(x = c(tab[4], tab[3]), y = c(tab[2], tab[1]))
## p-value < 2.2e-16
## alternative hypothesis: true odds ratio is greater than 1
## 95 percent confidence interval:
## 269.4737 Inf
## sample estimates:
## odds ratio
## 397.5212</code></pre>
<p><img src="bookdownproj_files/figure-html/unnamed-chunk-119-1.png" width="672" /></p>
</div>
</div>
<div id="promoter-4" class="section level4 unnumbered hasAnchor">
<h4>Promoter<a href="poe-hptm-enrichment-poe-transcription-dynamics.html#promoter-4" class="anchor-section" aria-label="Anchor link to header"></a></h4>
<div id="wl-9" class="section level5 unnumbered hasAnchor">
<h5>WL<a href="poe-hptm-enrichment-poe-transcription-dynamics.html#wl-9" class="anchor-section" aria-label="Anchor link to header"></a></h5>
<p>Gene:Peak (categories of allelic bias)</p>
<pre><code>##
## mat:mat mat:NA mat:pat NA:Lineage A NA:Lineage B NA:mat
## 2 4 3 59 63 156
## NA:NA NA:pat pat:mat pat:NA pat:pat
## 569 192 3 9 3</code></pre>
<p>Summary of overlaps (00 = neither peak nor gene biased, 01 = gene unbiased, peak biased, 10 = gene biased, peak unbiased, 11 = both gene and peak show allelic bias)</p>
<pre><code>##
## 00 01 10 11
## 1022 4 3 11</code></pre>
<p>Fishers exact test of enrichment (do genes showing allelic bias overlap with peaks showing allelic bias)?</p>
<pre><code>##
## Fisher's Exact Test for Count Data
##
## data: data.frame(x = c(tab[4], tab[3]), y = c(tab[2], tab[1]))
## p-value < 2.2e-16
## alternative hypothesis: true odds ratio is greater than 1
## 95 percent confidence interval:
## 189.0323 Inf
## sample estimates:
## odds ratio
## 830.8785</code></pre>
<p><img src="bookdownproj_files/figure-html/unnamed-chunk-125-1.png" width="672" /></p>
</div>
<div id="ql-9" class="section level5 unnumbered hasAnchor">
<h5>QL<a href="poe-hptm-enrichment-poe-transcription-dynamics.html#ql-9" class="anchor-section" aria-label="Anchor link to header"></a></h5>
<p>Gene:Peak (categories of allelic bias)</p>
<pre><code>##
## Lineage B:pat mat:NA mat:pat NA:Lineage A NA:Lineage B
## 1 1 5 99 92
## NA:mat NA:NA NA:pat pat:Lineage A pat:Lineage B
## 157 875 568 2 1
## pat:NA pat:pat
## 16 22</code></pre>
<p>Summary of overlaps (00 = neither peak nor gene biased, 01 = gene unbiased, peak biased, 10 = gene biased, peak unbiased, 11 = both gene and peak show allelic bias)</p>
<pre><code>##
## 00 01 10 11
## 1762 4 3 27</code></pre>
<p>Fishers exact test of enrichment (do genes showing allelic bias overlap with peaks showing allelic bias)?</p>
<pre><code>##
## Fisher's Exact Test for Count Data
##
## data: data.frame(x = c(tab[4], tab[3]), y = c(tab[2], tab[1]))
## p-value < 2.2e-16
## alternative hypothesis: true odds ratio is greater than 1
## 95 percent confidence interval:
## 857.3396 Inf
## sample estimates:
## odds ratio
## 3358.251</code></pre>
<p><img src="bookdownproj_files/figure-html/unnamed-chunk-131-1.png" width="672" /></p>
</div>
</div>
</div>
<div id="h3k4me3-5" class="section level3 unnumbered hasAnchor">
<h3>H3K4me3<a href="poe-hptm-enrichment-poe-transcription-dynamics.html#h3k4me3-5" class="anchor-section" aria-label="Anchor link to header"></a></h3>
<div id="gene-body-5" class="section level4 unnumbered hasAnchor">
<h4>Gene body<a href="poe-hptm-enrichment-poe-transcription-dynamics.html#gene-body-5" class="anchor-section" aria-label="Anchor link to header"></a></h4>
<div id="wl-10" class="section level5 unnumbered hasAnchor">
<h5>WL<a href="poe-hptm-enrichment-poe-transcription-dynamics.html#wl-10" class="anchor-section" aria-label="Anchor link to header"></a></h5>
<p>Gene:Peak (categories of allelic bias)</p>
<pre><code>##
## Lineage B:mat Lineage B:NA Lineage B:pat mat:Lineage A mat:Lineage B
## 2 7 3 5 1
## mat:mat mat:NA mat:pat NA:Lineage A NA:Lineage B
## 15 50 21 304 360
## NA:mat NA:NA NA:pat pat:Lineage A pat:Lineage B
## 1432 4824 2141 3 8
## pat:mat pat:NA pat:pat
## 37 84 33</code></pre>
<p>Summary of overlaps (00 = neither peak nor gene biased, 01 = gene unbiased, peak biased, 10 = gene biased, peak unbiased, 11 = both gene and peak show allelic bias)</p>
<pre><code>##
## 00 01 10 11
## 8806 27 127 106</code></pre>
<p>Fishers exact test of enrichment (do genes showing allelic bias overlap with peaks showing allelic bias)?</p>
<pre><code>##
## Fisher's Exact Test for Count Data
##
## data: data.frame(x = c(tab[4], tab[3]), y = c(tab[2], tab[1]))
## p-value < 2.2e-16
## alternative hypothesis: true odds ratio is greater than 1
## 95 percent confidence interval:
## 180.7667 Inf
## sample estimates:
## odds ratio
## 268.7595</code></pre>
<p><img src="bookdownproj_files/figure-html/unnamed-chunk-139-1.png" width="672" /></p>
</div>
<div id="ql-10" class="section level5 unnumbered hasAnchor">
<h5>QL<a href="poe-hptm-enrichment-poe-transcription-dynamics.html#ql-10" class="anchor-section" aria-label="Anchor link to header"></a></h5>
<p>Gene:Peak (categories of allelic bias)</p>
<pre><code>##
## Lineage B:Lineage A Lineage B:Lineage B Lineage B:mat Lineage B:NA
## 1 3 4 18
## Lineage B:pat mat:Lineage B mat:NA mat:pat
## 5 1 22 19
## NA:Lineage A NA:Lineage B NA:mat NA:NA
## 382 422 1003 5775
## NA:pat pat:Lineage A pat:Lineage B pat:mat
## 3836 3 4 5
## pat:NA pat:pat
## 79 89</code></pre>
<p>Summary of overlaps (00 = neither peak nor gene biased, 01 = gene unbiased, peak biased, 10 = gene biased, peak unbiased, 11 = both gene and peak show allelic bias)</p>
<pre><code>##
## 00 01 10 11
## 11206 25 81 113</code></pre>
<p>Fishers exact test of enrichment (do genes showing allelic bias overlap with peaks showing allelic bias)?</p>
<pre><code>##
## Fisher's Exact Test for Count Data
##
## data: data.frame(x = c(tab[4], tab[3]), y = c(tab[2], tab[1]))
## p-value < 2.2e-16
## alternative hypothesis: true odds ratio is greater than 1
## 95 percent confidence interval:
## 405.6765 Inf
## sample estimates:
## odds ratio
## 609.4468</code></pre>
<p><img src="bookdownproj_files/figure-html/unnamed-chunk-144-1.png" width="672" /></p>
</div>
</div>
<div id="promoter-5" class="section level4 unnumbered hasAnchor">
<h4>Promoter<a href="poe-hptm-enrichment-poe-transcription-dynamics.html#promoter-5" class="anchor-section" aria-label="Anchor link to header"></a></h4>
<div id="wl-11" class="section level5 unnumbered hasAnchor">
<h5>WL<a href="poe-hptm-enrichment-poe-transcription-dynamics.html#wl-11" class="anchor-section" aria-label="Anchor link to header"></a></h5>
<p>Gene:Peak (categories of allelic bias)</p>
<pre><code>##
## Lineage B:mat mat:mat mat:NA mat:pat NA:Lineage A
## 1 1 5 3 73
## NA:Lineage B NA:mat NA:NA NA:pat pat:Lineage A
## 50 247 781 363 1
## pat:mat pat:NA pat:pat
## 4 6 10</code></pre>
<p>Summary of overlaps (00 = neither peak nor gene biased, 01 = gene unbiased, peak biased, 10 = gene biased, peak unbiased, 11 = both gene and peak show allelic bias)</p>
<pre><code>##
## 00 01 10 11
## 1490 7 1 18</code></pre>
<p>Fishers exact test of enrichment (do genes showing allelic bias overlap with peaks showing allelic bias)?</p>
<pre><code>##
## Fisher's Exact Test for Count Data
##
## data: data.frame(x = c(tab[4], tab[3]), y = c(tab[2], tab[1]))
## p-value < 2.2e-16
## alternative hypothesis: true odds ratio is greater than 1
## 95 percent confidence interval:
## 538.9474 Inf
## sample estimates:
## odds ratio
## 3621.27</code></pre>
<p><img src="bookdownproj_files/figure-html/unnamed-chunk-150-1.png" width="672" /></p>
</div>
<div id="ql-11" class="section level5 unnumbered hasAnchor">
<h5>QL<a href="poe-hptm-enrichment-poe-transcription-dynamics.html#ql-11" class="anchor-section" aria-label="Anchor link to header"></a></h5>
<p>Gene:Peak (categories of allelic bias)</p>
<pre><code>##
## Lineage B:NA mat:NA mat:pat NA:Lineage A NA:Lineage B
## 2 2 6 66 69
## NA:mat NA:NA NA:pat pat:Lineage A pat:mat
## 132 925 645 1 4
## pat:NA pat:pat
## 15 17</code></pre>
<p>Summary of overlaps (00 = neither peak nor gene biased, 01 = gene unbiased, peak biased, 10 = gene biased, peak unbiased, 11 = both gene and peak show allelic bias)</p>
<pre><code>##
## 00 01 10 11