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<!DOCTYPE html>
<html xmlns="http://www.w3.org/1999/xhtml">
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<meta charset="utf-8">
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<meta name="generator" content="pandoc" />
<meta name="author" content="L Collado-Torres" />
<meta name="date" content="2016-04-12" />
<title>Example report using bumphunter results</title>
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<div id="header">
<h1 class="title">Example report using bumphunter results</h1>
<h4 class="author"><em>L Collado-Torres</em></h4>
<h4 class="date"><em>12 April 2016</em></h4>
</div>
<h4 class="package">Package version: <span style="font-weight: normal">regionReport 1.5.47</span></h4>
<h1>Contents</h1>
<div id="TOC">
<ul>
<li><a href="#bumphunter-example"><span class="toc-section-number">1</span> <em><a href="http://bioconductor.org/packages/bumphunter">bumphunter</a></em> example</a></li>
<li><a href="#reproducibility"><span class="toc-section-number">2</span> Reproducibility</a></li>
</ul>
</div>
<div id="bumphunter-example" class="section level1">
<h1><span class="header-section-number">1</span> <em><a href="http://bioconductor.org/packages/bumphunter">bumphunter</a></em> example</h1>
<p>The <em><a href="http://bioconductor.org/packages/bumphunter">bumphunter</a></em> package can be used for methylation analyses where you are interested in identifying differentially methylated regions. The <a href="http://bioconductor.org/packages/release/bioc/vignettes/bumphunter/inst/doc/bumphunter.pdf">vignette</a> explains in greater detail the data set we are using in this example.</p>
<pre class="r"><code>## Load bumphunter
library('bumphunter')</code></pre>
<pre><code>## Loading required package: S4Vectors</code></pre>
<pre><code>## Loading required package: stats4</code></pre>
<pre><code>## Loading required package: BiocGenerics</code></pre>
<pre><code>## Loading required package: parallel</code></pre>
<pre><code>##
## Attaching package: 'BiocGenerics'</code></pre>
<pre><code>## The following objects are masked from 'package:parallel':
##
## clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
## clusterExport, clusterMap, parApply, parCapply, parLapply,
## parLapplyLB, parRapply, parSapply, parSapplyLB</code></pre>
<pre><code>## The following objects are masked from 'package:stats':
##
## IQR, mad, xtabs</code></pre>
<pre><code>## The following objects are masked from 'package:base':
##
## anyDuplicated, append, as.data.frame, cbind, colnames,
## do.call, duplicated, eval, evalq, Filter, Find, get, grep,
## grepl, intersect, is.unsorted, lapply, lengths, Map, mapply,
## match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
## Position, rank, rbind, Reduce, rownames, sapply, setdiff,
## sort, table, tapply, union, unique, unsplit</code></pre>
<pre><code>##
## Attaching package: 'S4Vectors'</code></pre>
<pre><code>## The following objects are masked from 'package:base':
##
## colMeans, colSums, expand.grid, rowMeans, rowSums</code></pre>
<pre><code>## Loading required package: IRanges</code></pre>
<pre><code>## Loading required package: GenomeInfoDb</code></pre>
<pre><code>## Loading required package: GenomicRanges</code></pre>
<pre><code>## Loading required package: foreach</code></pre>
<pre><code>## foreach: simple, scalable parallel programming from Revolution Analytics
## Use Revolution R for scalability, fault tolerance and more.
## http://www.revolutionanalytics.com</code></pre>
<pre><code>## Loading required package: iterators</code></pre>
<pre><code>## Loading required package: locfit</code></pre>
<pre><code>## locfit 1.5-9.1 2013-03-22</code></pre>
<pre class="r"><code>## Create data from the vignette
pos <- list(pos1=seq(1, 1000, 35),
pos2=seq(2001, 3000, 35),
pos3=seq(1, 1000, 50))
chr <- rep(paste0('chr', c(1, 1, 2)), times = sapply(pos, length))
pos <- unlist(pos, use.names = FALSE)
## Find clusters
cl <- clusterMaker(chr, pos, maxGap = 300)
## Build simulated bumps
Indexes <- split(seq_along(cl), cl)
beta1 <- rep(0, length(pos))
for(i in seq(along=Indexes)){
ind <- Indexes[[i]]
x <- pos[ind]
z <- scale(x, median(x), max(x)/12)
beta1[ind] <- i*(-1)^(i+1)*pmax(1-abs(z)^3,0)^3 ##multiply by i to vary size
}
## Build data
beta0 <- 3 * sin(2 * pi * pos / 720)
X <- cbind(rep(1, 20), rep(c(0, 1), each = 10))
set.seed(23852577)
error <- matrix(rnorm(20 * length(beta1), 0, 1), ncol = 20)
y <- t(X[, 1]) %x% beta0 + t(X[, 2]) %x% beta1 + error
## Perform bumphunting
tab <- bumphunter(y, X, chr, pos, cl, cutoff=.5)</code></pre>
<pre><code>## [bumphunterEngine] Using a single core (backend: doSEQ, version: 1.4.3).</code></pre>
<pre><code>## [bumphunterEngine] Computing coefficients.</code></pre>
<pre><code>## [bumphunterEngine] Finding regions.</code></pre>
<pre><code>## [bumphunterEngine] Found 15 bumps.</code></pre>
<pre class="r"><code>## Explore data
lapply(tab, head)</code></pre>
<pre><code>## $table
## chr start end value area cluster indexStart indexEnd L
## 10 chr1 2316 2631 -1.5814747 15.8147473 2 39 48 10
## 7 chr2 451 551 1.5891293 4.7673878 3 68 70 3
## 2 chr1 456 526 1.0678828 3.2036485 1 14 16 3
## 5 chr1 2176 2211 0.7841794 1.5683589 2 35 36 2
## 6 chr1 2841 2841 1.2010184 1.2010184 2 54 54 1
## 4 chr1 771 771 0.7780902 0.7780902 1 23 23 1
## clusterL
## 10 29
## 7 20
## 2 29
## 5 29
## 6 29
## 4 29
##
## $coef
## [,1]
## [1,] 0.60960932
## [2,] -0.09052769
## [3,] -0.21482638
## [4,] 0.13053755
## [5,] -0.21723642
## [6,] 0.39934961
##
## $fitted
## [,1]
## [1,] 0.60960932
## [2,] -0.09052769
## [3,] -0.21482638
## [4,] 0.13053755
## [5,] -0.21723642
## [6,] 0.39934961
##
## $pvaluesMarginal
## [1] NA</code></pre>
<p>Once we have the regions we can proceed to build the required <code>GRanges</code> object.</p>
<pre class="r"><code>library('GenomicRanges')
## Build GRanges with sequence lengths
regions <- GRanges(seqnames = tab$table$chr,
IRanges(start = tab$table$start, end = tab$table$end),
strand = '*', value = tab$table$value, area = tab$table$area,
cluster = tab$table$cluster, L = tab$table$L, clusterL = tab$table$clusterL)
## Assign chr lengths
data(hg19Ideogram, package = 'biovizBase')
seqlengths(regions) <- seqlengths(hg19Ideogram)[names(seqlengths(regions))]
## Explore the regions
regions</code></pre>
<pre><code>## GRanges object with 15 ranges and 5 metadata columns:
## seqnames ranges strand | value area
## <Rle> <IRanges> <Rle> | <numeric> <numeric>
## [1] chr1 [2316, 2631] * | -1.58147472668612 15.8147472668612
## [2] chr2 [ 451, 551] * | 1.58912926544627 4.76738779633882
## [3] chr1 [ 456, 526] * | 1.06788283103948 3.20364849311844
## [4] chr1 [2176, 2211] * | 0.784179442360784 1.56835888472157
## [5] chr1 [2841, 2841] * | 1.20101842543356 1.20101842543356
## ... ... ... ... . ... ...
## [11] chr1 [ 631, 631] * | 0.618602646982714 0.618602646982714
## [12] chr1 [ 1, 1] * | 0.609609318450113 0.609609318450113
## [13] chr1 [2911, 2911] * | -0.576423040796044 0.576423040796044
## [14] chr2 [ 251, 251] * | -0.556159535339166 0.556159535339166
## [15] chr1 [2806, 2806] * | -0.521605772372843 0.521605772372843
## cluster L clusterL
## <numeric> <numeric> <integer>
## [1] 2 10 29
## [2] 3 3 20
## [3] 1 3 29
## [4] 2 2 29
## [5] 2 1 29
## ... ... ... ...
## [11] 1 1 29
## [12] 1 1 29
## [13] 2 1 29
## [14] 3 1 20
## [15] 2 1 29
## -------
## seqinfo: 2 sequences from an unspecified genome</code></pre>
<p>Now that we have identified a set of differentially methylated regions we can proceed to creating the HTML report. Note that this report has less information than the <a href="http://leekgroup.github.io/regionReportSupp/DiffBind.html">DiffBind example</a> because we don’t have a p-value variable.</p>
<pre class="r"><code>## Load regionReport
library('regionReport')</code></pre>
<pre class="r"><code>## Make it so that the report will be available as a vignette
original <- readLines(system.file('regionExploration', 'regionExploration.Rmd',
package = 'regionReport'))
vignetteInfo <- c(
'vignette: >',
' %\\VignetteEngine{knitr::rmarkdown}',
' %\\VignetteIndexEntry{Basic genomic regions exploration}',
' %\\VignetteEncoding{UTF-8}'
)
new <- c(original[1:12], vignetteInfo, original[13:length(original)])
writeLines(new, '/Users/lcollado/Dropbox/JHSPH/Code/regionReportSupp/bumphunter-example/regionReportBumphunter.Rmd')
## Now create the report
report <- renderReport(regions, 'Example bumphunter', pvalueVars = NULL,
densityVars = c('Area' = 'area', 'Value' = 'value',
'Cluster Length' = 'clusterL'), significantVar = NULL,
output = 'index', outdir = 'bumphunter-example',
template = '/Users/lcollado/Dropbox/JHSPH/Code/regionReportSupp/bumphunter-example/regionReportBumphunter.Rmd', device = 'png')</code></pre>
<pre><code>## Warning: replacing previous import 'ggplot2::Position' by
## 'BiocGenerics::Position' when loading 'ggbio'</code></pre>
<pre><code>## Writing 11 Bibtex entries ...</code></pre>
<pre><code>## OK
## Results written to file 'bumphunter-example/index.bib'</code></pre>
<pre><code>##
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<pre><code>## No annotationPackage supplied. Trying org.Hs.eg.db.</code></pre>
<pre><code>## Loading required package: org.Hs.eg.db</code></pre>
<pre><code>## Loading required package: DBI</code></pre>
<pre><code>## </code></pre>
<pre><code>## Getting TSS and TSE.</code></pre>
<pre><code>## Getting CSS and CSE.</code></pre>
<pre><code>## Getting exons.</code></pre>
<pre><code>## Annotating genes.</code></pre>
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## ordinary text without R code</code></pre>
<pre><code>## output file: index.knit.md</code></pre>
<pre><code>## /usr/local/bin/pandoc +RTS -K512m -RTS index.utf8.md --to html --from markdown+autolink_bare_uris+ascii_identifiers+tex_math_single_backslash-implicit_figures --output index.html --smart --email-obfuscation none --self-contained --standalone --section-divs --table-of-contents --toc-depth 3 --variable toc_float=1 --variable toc_selectors=h1,h2,h3 --variable toc_collapsed=1 --variable toc_smooth_scroll=1 --template /Library/Frameworks/R.framework/Versions/3.3/Resources/library/rmarkdown/rmd/h/default.html --variable 'theme:spacelab' --include-in-header /var/folders/cx/n9s558kx6fb7jf5z_pgszgb80000gn/T//Rtmp41dyxK/rmarkdown-str3a9461833679.html --mathjax --variable 'mathjax-url:https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --no-highlight --variable highlightjs=/Library/Frameworks/R.framework/Versions/3.3/Resources/library/rmarkdown/rmd/h/highlight --variable navigationjs=/Library/Frameworks/R.framework/Versions/3.3/Resources/library/rmarkdown/rmd/h/navigation-1.0 --variable code_folding=hide</code></pre>
<pre><code>##
## Output created: index.html</code></pre>
<pre class="r"><code>## Clean up
file.remove('/Users/lcollado/Dropbox/JHSPH/Code/regionReportSupp/bumphunter-example/regionReportBumphunter.Rmd')</code></pre>
<pre><code>## [1] TRUE</code></pre>
<p>You can view the final report <a href="/regionReportSupp/bumphunter-example/index.html">here</a>.</p>
</div>
<div id="reproducibility" class="section level1">
<h1><span class="header-section-number">2</span> Reproducibility</h1>
<pre class="r"><code>## Date generated:
Sys.time()</code></pre>
<pre><code>## [1] "2016-04-12 07:36:20 EDT"</code></pre>
<pre class="r"><code>## Time spent making this page:
proc.time()</code></pre>
<pre><code>## user system elapsed
## 172.555 7.336 200.023</code></pre>
<pre class="r"><code>## R and packages info:
options(width = 120)
devtools::session_info()</code></pre>
<pre><code>## Session info -----------------------------------------------------------------------------------------------------------</code></pre>
<pre><code>## setting value
## version R version 3.3.0 alpha (2016-03-23 r70368)
## system x86_64, darwin13.4.0
## ui AQUA
## language (EN)
## collate en_US.UTF-8
## tz America/New_York
## date 2016-04-12</code></pre>
<pre><code>## Packages ---------------------------------------------------------------------------------------------------------------</code></pre>
<pre><code>## package * version date source
## acepack 1.3-3.3 2014-11-24 CRAN (R 3.3.0)
## annotate 1.49.1 2016-02-06 Bioconductor
## AnnotationDbi * 1.33.8 2016-04-10 Bioconductor
## AnnotationHub 2.3.16 2016-03-25 Bioconductor
## backports 1.0.2 2016-03-18 CRAN (R 3.3.0)
## bibtex 0.4.0 2014-12-31 CRAN (R 3.3.0)
## Biobase * 2.31.3 2016-01-14 Bioconductor
## BiocGenerics * 0.17.4 2016-04-07 Bioconductor
## BiocInstaller 1.21.4 2016-03-23 Bioconductor
## BiocParallel 1.5.21 2016-03-23 Bioconductor
## BiocStyle * 1.99.0 2016-04-05 Bioconductor
## biomaRt 2.27.2 2016-01-14 Bioconductor
## Biostrings 2.39.12 2016-02-21 Bioconductor
## biovizBase 1.19.6 2016-04-06 Bioconductor
## bitops 1.0-6 2013-08-17 CRAN (R 3.3.0)
## BSgenome 1.39.4 2016-02-21 Bioconductor
## bumphunter * 1.11.5 2016-03-29 Bioconductor
## checkmate 1.7.4 2016-04-08 CRAN (R 3.3.0)
## cluster 2.0.3 2015-07-21 CRAN (R 3.3.0)
## codetools 0.2-14 2015-07-15 CRAN (R 3.3.0)
## colorspace 1.2-6 2015-03-11 CRAN (R 3.3.0)
## DBI * 0.3.1 2014-09-24 CRAN (R 3.3.0)
## DEFormats 0.99.8 2016-03-31 Bioconductor
## derfinder * 1.5.30 2016-03-25 Bioconductor
## derfinderHelper 1.5.3 2016-03-23 Bioconductor
## derfinderPlot * 1.5.7 2016-03-23 Bioconductor
## DESeq2 1.11.42 2016-04-10 Bioconductor
## devtools * 1.10.0 2016-01-23 CRAN (R 3.3.0)
## dichromat 2.0-0 2013-01-24 CRAN (R 3.3.0)
## digest 0.6.9 2016-01-08 CRAN (R 3.3.0)
## doRNG 1.6 2014-03-07 CRAN (R 3.3.0)
## DT * 0.1 2015-06-09 CRAN (R 3.3.0)
## edgeR 3.13.8 2016-04-08 Bioconductor
## ensembldb 1.3.19 2016-04-03 Bioconductor
## evaluate 0.8.3 2016-03-05 CRAN (R 3.3.0)
## foreach * 1.4.3 2015-10-13 CRAN (R 3.3.0)
## foreign 0.8-66 2015-08-19 CRAN (R 3.3.0)
## formatR 1.3 2016-03-05 CRAN (R 3.3.0)
## Formula 1.2-1 2015-04-07 CRAN (R 3.3.0)
## genefilter 1.53.3 2016-03-23 Bioconductor
## geneplotter 1.49.0 2016-01-14 Bioconductor
## GenomeInfoDb * 1.7.6 2016-01-29 Bioconductor
## GenomicAlignments 1.7.20 2016-02-25 Bioconductor
## GenomicFeatures * 1.23.29 2016-04-05 Bioconductor
## GenomicFiles 1.7.9 2016-02-22 Bioconductor
## GenomicRanges * 1.23.25 2016-03-31 Bioconductor
## GGally 1.0.1 2016-01-14 CRAN (R 3.3.0)
## ggbio * 1.19.13 2016-04-03 Bioconductor
## ggplot2 * 2.1.0 2016-03-01 CRAN (R 3.3.0)
## graph 1.49.1 2016-01-14 Bioconductor
## gridExtra * 2.2.1 2016-02-29 CRAN (R 3.3.0)
## gtable 0.2.0 2016-02-26 CRAN (R 3.3.0)
## highr 0.5.1 2015-09-18 CRAN (R 3.3.0)
## Hmisc 3.17-3 2016-04-03 CRAN (R 3.3.0)
## htmltools 0.3.5 2016-03-21 CRAN (R 3.3.0)
## htmlwidgets 0.6 2016-02-25 CRAN (R 3.3.0)
## httpuv 1.3.3 2015-08-04 CRAN (R 3.3.0)
## httr 1.1.0 2016-01-28 CRAN (R 3.3.0)
## interactiveDisplayBase 1.9.0 2016-01-14 Bioconductor
## IRanges * 2.5.43 2016-04-10 Bioconductor
## iterators * 1.0.8 2015-10-13 CRAN (R 3.3.0)
## jsonlite 0.9.19 2015-11-28 CRAN (R 3.3.0)
## knitcitations 1.0.7 2015-10-28 CRAN (R 3.3.0)
## knitr * 1.12.3 2016-01-22 CRAN (R 3.3.0)
## knitrBootstrap 1.0.0 2016-03-24 Github (jimhester/knitrBootstrap@cdaa4a9)
## labeling 0.3 2014-08-23 CRAN (R 3.3.0)
## lattice 0.20-33 2015-07-14 CRAN (R 3.3.0)
## latticeExtra 0.6-28 2016-02-09 CRAN (R 3.3.0)
## limma 3.27.14 2016-03-23 Bioconductor
## locfit * 1.5-9.1 2013-04-20 CRAN (R 3.3.0)
## lubridate 1.5.6 2016-04-06 CRAN (R 3.3.0)
## magrittr 1.5 2014-11-22 CRAN (R 3.3.0)
## markdown 0.7.7 2015-04-22 CRAN (R 3.3.0)
## Matrix 1.2-4 2016-03-02 CRAN (R 3.3.0)
## matrixStats 0.50.1 2015-12-15 CRAN (R 3.3.0)
## memoise 1.0.0 2016-01-29 CRAN (R 3.3.0)
## mgcv * 1.8-12 2016-03-03 CRAN (R 3.3.0)
## mime 0.4 2015-09-03 CRAN (R 3.3.0)
## munsell 0.4.3 2016-02-13 CRAN (R 3.3.0)
## nlme * 3.1-126 2016-03-14 CRAN (R 3.3.0)
## nnet 7.3-12 2016-02-02 CRAN (R 3.3.0)
## org.Hs.eg.db * 3.3.0 2016-04-11 Bioconductor
## OrganismDbi 1.13.6 2016-04-05 Bioconductor
## pkgmaker 0.22 2014-05-14 CRAN (R 3.3.0)
## plyr 1.8.3 2015-06-12 CRAN (R 3.3.0)
## qvalue 2.3.2 2016-01-14 Bioconductor
## R6 2.1.2 2016-01-26 CRAN (R 3.3.0)
## RBGL 1.47.0 2016-01-14 Bioconductor
## RColorBrewer * 1.1-2 2014-12-07 CRAN (R 3.3.0)
## Rcpp 0.12.4 2016-03-26 CRAN (R 3.3.0)
## RCurl 1.95-4.8 2016-03-01 CRAN (R 3.3.0)
## RefManageR 0.10.13 2016-04-04 CRAN (R 3.3.0)
## regionReport * 1.5.47 2016-04-12 Bioconductor
## registry 0.3 2015-07-08 CRAN (R 3.3.0)
## reshape 0.8.5 2014-04-23 CRAN (R 3.3.0)
## reshape2 1.4.1 2014-12-06 CRAN (R 3.3.0)
## RJSONIO 1.3-0 2014-07-28 CRAN (R 3.3.0)
## rmarkdown 0.9.5 2016-02-22 CRAN (R 3.3.0)
## rngtools 1.2.4 2014-03-06 CRAN (R 3.3.0)
## rpart 4.1-10 2015-06-29 CRAN (R 3.3.0)
## Rsamtools 1.23.8 2016-04-10 Bioconductor
## RSQLite * 1.0.0 2014-10-25 CRAN (R 3.3.0)
## rstudioapi 0.5 2016-01-24 CRAN (R 3.3.0)
## rtracklayer 1.31.10 2016-04-07 Bioconductor
## S4Vectors * 0.9.46 2016-04-07 Bioconductor
## scales 0.4.0 2016-02-26 CRAN (R 3.3.0)
## shiny 0.13.2 2016-03-28 CRAN (R 3.3.0)
## stringi 1.0-1 2015-10-22 CRAN (R 3.3.0)
## stringr 1.0.0 2015-04-30 CRAN (R 3.3.0)
## SummarizedExperiment 1.1.23 2016-04-06 Bioconductor
## survival 2.38-3 2015-07-02 CRAN (R 3.3.0)
## TxDb.Hsapiens.UCSC.hg19.knownGene * 3.2.2 2016-03-24 Bioconductor
## VariantAnnotation 1.17.23 2016-04-07 Bioconductor
## whisker * 0.3-2 2013-04-28 CRAN (R 3.3.0)
## XML 3.98-1.4 2016-03-01 CRAN (R 3.3.0)
## xtable 1.8-2 2016-02-05 CRAN (R 3.3.0)
## XVector 0.11.8 2016-04-06 Bioconductor
## yaml 2.1.13 2014-06-12 CRAN (R 3.3.0)
## zlibbioc 1.17.1 2016-03-19 Bioconductor</code></pre>
</div>
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