If you wish, you can view this vignette online here.
regionReport
(Collado-Torres, Jaffe, and Leek, 2014)
creates HTML reports
styled with knitrBootstrap
(Hester, 2013)
for
a set of regions such as derfinder
(Collado-Torres, Frazee, Jaffe, and Leek, 2014)
results.
Currently, this package includes a basic exploration analysis of derfinder
results which we expect users to be interested in reproducing with their own
data. The analysis is written in R Markdown
format and derfinderReport()
takes the results from
derfinder
, performs a couple of setup operations, and then relies on
knitr
(Xie, 2014)
, rmarkdown
(Allaire, McPherson, Xie, Wickham, et al., 2014)
, and knitrBootstrap
(Hester, 2013)
for generating the report.
regionReport
This is currently under construction.
derfinder
caseGoodies in this report are powered by ggbio
(Yin, Cook, and Lawrence, 2012)
and ggplot2
(Wickham, 2009)
.
derfinder
Prior to using regionReport::derfinderReport()
you must use derfinder
to analyze a specific
data set. While there are many ways to do so, we recommend using
analyzeChr() with the same prefix argument. Then merging the results with
mergeResults().
Below, we run derfinder
for the example data included in the package. The
steps are:
## Load derfinder library('derfinder') ## The output will be saved in the 'report' directory dir.create('report', showWarnings = FALSE, recursive = TRUE)
The following code runs derfinder
.
## Save the current path initialPath <- getwd() setwd(file.path(initialPath, 'report')) ## Generate output from derfinder ## Collapse the coverage information collapsedFull <- collapseFullCoverage(list(genomeData$coverage), verbose=TRUE) ## Calculate library size adjustments sampleDepths <- sampleDepth(collapsedFull, probs=c(0.5), nonzero=TRUE, verbose=TRUE) ## Build the models group <- genomeInfo$pop adjustvars <- data.frame(genomeInfo$gender) models <- makeModels(sampleDepths, testvars=group, adjustvars=adjustvars) ## Analyze chromosome 21 analysis <- analyzeChr(chr='21', coverageInfo=genomeData, models=models, cutoffFstat=1, cutoffType='manual', seeds=20140330, groupInfo=group, mc.cores=1, writeOutput=TRUE, returnOutput=TRUE) ## Save the stats options for later optionsStats <- analysis$optionsStats ## Change the directory back to the original one setwd(initialPath)
For convenience, we have included the derfinder
results as part of
regionReport
. Note that the above functions are routinely checked as part
of derfinder
.
## Copy previous results file.copy(system.file(file.path('extdata', 'chr21'), package='derfinder', mustWork=TRUE), 'report', recursive=TRUE)
## [1] TRUE
Next, proceed to merging the results.
## Merge the results from the different chromosomes. In this case, there's ## only one: chr21 mergeResults(chrs = 'chr21', prefix = 'report', genomicState = genomicState$fullGenome)
Once the derfinder
output has been generated and merged, use
derfinderReport() to create the HTML report.
## Load derfindeReport library('regionReport')
## Generate the HTML report report <- derfinderReport(prefix='report', browse=FALSE, nBestRegions=15, makeBestClusters=TRUE, outdir='html', fullCov=list('21'=genomeDataRaw$coverage), optionsStats=optionsStats)
Once the output is generated, you can browse the report from R
using
browseURL() as shown below.
## Browse the report browseURL(report)
You can compare the resulting report with the pre-compiled report using the following code.
browseURL(system.file(file.path('basicExploration', 'basicExploration.html'), package = 'regionReport', mustWork = TRUE))
Note that the reports require an active Internet connection to render correctly.
The report is self-explanatory and will change some of the text depending on the input options.
If the report is taking too long to compile (say more than 3 hours), you might
want to consider setting nBestCluters to a small number or even set
makeBestClusters to FALSE
.
If you are interested in using the advanced arguments, use derfinder::advancedArg()
as shown below:
## URLs to advanced arguemtns derfinder::advancedArg('derfinderReport', package = 'regionReport', browse = FALSE) ## Set browse = TRUE if you want to open them in your browser
This package was made possible thanks to:
(R Core Team, 2014)
(Collado-Torres, Frazee, Jaffe, and Leek, 2014)
(Collado-Torres, Jaffe, and Leek, 2014)
(Wickham and Chang, 2014)
(Arora, Morgan, Carlson, and Pages, 2014)
(Lawrence, Huber, Pagès, Aboyoun, et al., 2013)
(Yin, Cook, and Lawrence, 2012)
(Wickham, 2009)
(R Core Team, 2014)
(Auguie, 2012)
(Lawrence, Huber, Pagès, Aboyoun, et al., 2013)
(Boettiger, 2014)
(Xie, 2014)
(Hester, 2013)
(Neuwirth, 2011)
(Allaire, McPherson, Xie, Wickham, et al., 2014)
(Yin, Lawrence, and Cook, 2014)
(Urbanek and Horner, 2014)
(Carlson, 2014)
Code for creating the vignette
## Create the vignette library('knitrBootstrap') knitrBootstrapFlag <- packageVersion('knitrBootstrap') < '1.0.0' if(knitrBootstrapFlag) { ## CRAN version system.time(knit_bootstrap('regionReport.Rmd', chooser=c('boot', 'code'), show_code = TRUE)) unlink('regionReport.md') } else { ## GitHub version library('rmarkdown') system.time(render('regionReport.Rmd', 'knitrBootstrap::bootstrap_document')) } ## Note: if you prefer the knitr version use: # library('rmarkdown') # system.time(render('regionReport.Rmd', 'html_document')) ## Extract the R code library('knitr') knit('regionReport.Rmd', tangle = TRUE) ## Copy report output to be distributed with the package for comparison ## purposes if(gsub('.*/', '', getwd()) == 'realVignettes') { file.copy(file.path('report', 'html', 'basicExploration.html'), file.path('..', '..', 'inst', 'basicExploration', 'basicExploration.html'), overwrite=TRUE) } else { file.copy(file.path('report', 'html', 'basicExploration.html'), file.path('..', 'inst', 'basicExploration', 'basicExploration.html'), overwrite=TRUE) } ## Clean up file.remove('regionReportRef.bib') #unlink('regionReport_files', recursive=TRUE) unlink('report', recursive = TRUE)
Date the vignette was generated.
## [1] "2014-11-05 22:10:22 PST"
Wallclock time spent generating the vignette.
## Time difference of 1.185 mins
R
session information.
## setting value ## version R Under development (unstable) (2014-11-03 r66928) ## system x86_64, linux-gnu ## ui X11 ## language en_US: ## collate C ## tz
## package * version date source ## AnnotationDbi 1.29.1 2014-11-06 Bioconductor ## BBmisc 1.8 2014-10-30 CRAN (R 3.2.0) ## BSgenome 1.35.5 2014-11-06 Bioconductor ## BatchJobs 1.5 2014-10-30 CRAN (R 3.2.0) ## Biobase 2.27.0 2014-11-06 Bioconductor ## BiocGenerics 0.13.0 2014-11-06 Bioconductor ## BiocParallel 1.1.5 2014-11-06 Bioconductor ## Biostrings 2.35.2 2014-11-06 Bioconductor ## DBI 0.3.1 2014-09-24 CRAN (R 3.2.0) ## Formula 1.1.2 2014-07-13 CRAN (R 3.2.0) ## GGally 0.4.8 2014-08-26 CRAN (R 3.2.0) ## GenomeInfoDb 1.3.6 2014-11-06 Bioconductor ## GenomicAlignments 1.3.5 2014-11-06 Bioconductor ## GenomicFeatures 1.19.6 2014-11-06 Bioconductor ## GenomicFiles 1.3.8 2014-11-06 Bioconductor ## GenomicRanges 1.19.4 2014-11-06 Bioconductor ## Hmisc 3.14.5 2014-09-12 CRAN (R 3.2.0) ## IRanges 2.1.6 2014-11-06 Bioconductor ## MASS 7.3.35 2014-09-30 CRAN (R 3.2.0) ## Matrix 1.1.4 2014-06-15 CRAN (R 3.2.0) ## OrganismDbi 1.9.0 2014-11-06 Bioconductor ## R.methodsS3 1.6.1 2014-01-05 CRAN (R 3.2.0) ## RBGL 1.43.0 2014-11-06 Bioconductor ## RColorBrewer 1.0.5 2011-06-17 CRAN (R 3.2.0) ## RCurl 1.95.4.3 2014-07-29 CRAN (R 3.2.0) ## RJSONIO 1.3.0 2014-07-28 CRAN (R 3.2.0) ## RSQLite 1.0.0 2014-10-25 CRAN (R 3.2.0) ## Rcpp 0.11.3 2014-09-29 CRAN (R 3.2.0) ## RefManageR 0.8.40 2014-10-29 CRAN (R 3.2.0) ## Rsamtools 1.19.8 2014-11-06 Bioconductor ## S4Vectors 0.5.4 2014-11-06 Bioconductor ## VariantAnnotation 1.13.6 2014-11-06 Bioconductor ## XML 3.98.1.1 2013-06-20 CRAN (R 3.2.0) ## XVector 0.7.2 2014-11-06 Bioconductor ## acepack 1.3.3.3 2013-05-03 CRAN (R 3.2.0) ## base64enc 0.1.2 2014-06-26 CRAN (R 3.2.0) ## bibtex 0.3.6 2013-07-29 CRAN (R 3.2.0) ## biomaRt 2.23.0 2014-11-06 Bioconductor ## biovizBase 1.15.0 2014-11-06 Bioconductor ## bitops 1.0.6 2013-08-17 CRAN (R 3.2.0) ## brew 1.0.6 2011-04-13 CRAN (R 3.2.0) ## bumphunter 1.7.0 2014-11-06 Bioconductor ## checkmate 1.5.0 2014-10-19 CRAN (R 3.2.0) ## cluster 1.15.3 2014-09-04 CRAN (R 3.2.0) ## codetools 0.2.9 2014-08-21 CRAN (R 3.2.0) ## colorspace 1.2.4 2013-09-30 CRAN (R 3.2.0) ## derfinder * 1.1.9 2014-11-06 Bioconductor ## derfinderHelper 1.1.5 2014-11-06 Bioconductor ## derfinderPlot 1.1.5 2014-11-06 Bioconductor ## devtools * 1.6.1 2014-10-07 CRAN (R 3.2.0) ## dichromat 2.0.0 2013-01-24 CRAN (R 3.2.0) ## digest 0.6.4 2013-12-03 CRAN (R 3.2.0) ## doRNG 1.6 2014-03-07 CRAN (R 3.2.0) ## evaluate 0.5.5 2014-04-29 CRAN (R 3.2.0) ## fail 1.2 2013-09-19 CRAN (R 3.2.0) ## foreach 1.4.2 2014-04-11 CRAN (R 3.2.0) ## foreign 0.8.61 2014-03-28 CRAN (R 3.2.0) ## formatR 1.0 2014-08-25 CRAN (R 3.2.0) ## ggbio 1.15.0 2014-11-06 Bioconductor ## ggplot2 1.0.0 2014-05-21 CRAN (R 3.2.0) ## graph 1.45.0 2014-11-06 Bioconductor ## gridExtra 0.9.1 2012-08-09 CRAN (R 3.2.0) ## gtable 0.1.2 2012-12-05 CRAN (R 3.2.0) ## htmltools 0.2.6 2014-09-08 CRAN (R 3.2.0) ## httr 0.5 2014-09-02 CRAN (R 3.2.0) ## iterators 1.0.7 2014-04-11 CRAN (R 3.2.0) ## knitcitations * 1.0.4 2014-10-28 CRAN (R 3.2.0) ## knitr 1.7 2014-10-13 CRAN (R 3.2.0) ## knitrBootstrap * 0.9.0 2013-10-17 CRAN (R 3.2.0) ## lattice 0.20.29 2014-04-04 CRAN (R 3.2.0) ## latticeExtra 0.6.26 2013-08-15 CRAN (R 3.2.0) ## locfit 1.5.9.1 2013-04-20 CRAN (R 3.2.0) ## lubridate 1.3.3 2013-12-31 CRAN (R 3.2.0) ## markdown 0.7.4 2014-08-24 CRAN (R 3.2.0) ## matrixStats 0.10.3 2014-10-15 CRAN (R 3.2.0) ## memoise 0.2.1 2014-04-22 CRAN (R 3.2.0) ## mgcv 1.8.3 2014-08-29 CRAN (R 3.2.0) ## munsell 0.4.2 2013-07-11 CRAN (R 3.2.0) ## nlme 3.1.118 2014-10-07 CRAN (R 3.2.0) ## nnet 7.3.8 2014-03-28 CRAN (R 3.2.0) ## pkgmaker 0.22 2014-05-14 CRAN (R 3.2.0) ## plyr 1.8.1 2014-02-26 CRAN (R 3.2.0) ## proto 0.3.10 2012-12-22 CRAN (R 3.2.0) ## qvalue 1.41.0 2014-11-06 Bioconductor ## regionReport * 1.1.6 2014-11-06 Bioconductor ## registry 0.2 2012-01-24 CRAN (R 3.2.0) ## reshape 0.8.5 2014-04-23 CRAN (R 3.2.0) ## reshape2 1.4 2014-04-23 CRAN (R 3.2.0) ## rmarkdown 0.3.3 2014-09-17 CRAN (R 3.2.0) ## rngtools 1.2.4 2014-03-06 CRAN (R 3.2.0) ## rpart 4.1.8 2014-03-28 CRAN (R 3.2.0) ## rstudioapi 0.1 2014-03-27 CRAN (R 3.2.0) ## rtracklayer 1.27.3 2014-11-06 Bioconductor ## scales 0.2.4 2014-04-22 CRAN (R 3.2.0) ## sendmailR 1.2.1 2014-09-21 CRAN (R 3.2.0) ## stringr 0.6.2 2012-12-06 CRAN (R 3.2.0) ## survival 2.37.7 2014-01-22 CRAN (R 3.2.0) ## xtable 1.7.4 2014-09-12 CRAN (R 3.2.0) ## zlibbioc 1.13.0 2014-11-06 Bioconductor
This vignette was generated using knitrBootstrap
(Hester, 2013)
with knitr
(Xie, 2014)
and rmarkdown
(Allaire, McPherson, Xie, Wickham, et al., 2014)
running behind the scenes.
Citations made with knitcitations
(Boettiger, 2014)
.
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[2] S. Arora, M. Morgan, M. Carlson and H. Pages. GenomeInfoDb: Utilities for manipulating chromosome and other 'seqname' identifiers. R package version 1.3.6. 2014.
[3] B. Auguie. gridExtra: functions in Grid graphics. R package version 0.9.1. 2012. URL: http://CRAN.R-project.org/package=gridExtra.
[4] C. Boettiger. knitcitations: Citations for knitr markdown files. R package version 1.0.4. 2014. URL: http://CRAN.R-project.org/package=knitcitations.
[5] M. Carlson. TxDb.Hsapiens.UCSC.hg19.knownGene: Annotation package for TxDb object(s). R package version 3.0.0. 2014.
[6] L. Collado-Torres, A. C. Frazee, A. E. Jaffe and J. T. Leek. derfinder: Annotation-agnostic differential expression analysis of RNA-seq data at base-pair resolution. https://github.com/lcolladotor/derfinder - R package version 1.1.9. 2014. URL: http://www.bioconductor.org/packages/release/bioc/html/derfinder.html.
[7] L. Collado-Torres, A. E. Jaffe and J. T. Leek. derfinderPlot: Plotting functions for derfinder. https://github.com/lcolladotor/derfinderPlot - R package version 1.1.5. 2014. URL: http://www.bioconductor.org/packages/release/bioc/html/derfinderPlot.html.
[8] L. Collado-Torres, A. E. Jaffe and J. T. Leek. regionReport: Generate HTML reports for exploring a set of regions. https://github.com/lcolladotor/regionReport - R package version 1.1.6. 2014. URL: http://www.bioconductor.org/packages/release/bioc/html/regionReport.html.
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[14] H. Wickham. ggplot2: elegant graphics for data analysis. Springer New York, 2009. ISBN: 978-0-387-98140-6. URL: http://had.co.nz/ggplot2/book.
[15] H. Wickham and W. Chang. devtools: Tools to make developing R code easier. R package version 1.6.1. 2014. URL: http://CRAN.R-project.org/package=devtools.
[16] Y. Xie. “knitr: A Comprehensive Tool for Reproducible Research in R”. In: Implementing Reproducible Computational Research. Ed. by V. Stodden, F. Leisch and R. D. Peng. ISBN 978-1466561595. Chapman and Hall/CRC, 2014. URL: http://www.crcpress.com/product/isbn/9781466561595.
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