regionReport has a specific template for
DESeq2 results. The file DESEq2.html shows how to create a HTML and a PDF report using results from
DESeq2. The resulting HTML report is available at DESeq2-example and the PDF version at DESeq2Report.
regionReport can use
edgeR results to create reports that look nearly identical to the reports from
DESeq2 results along with some
edgeR specific plots. The file edgeR.html shows how to create a HTML and a PDF report using results from
edgeR. The resulting HTML report is available at edgeR-example and the PDF version at edgerReport. The file edgeR.html also creates a HTML report for
edgeR-robust results available at edgeR-robust-example.
An example using bumphunter is showcased at bumphunterExample.html. This file shows the code for obtaining a set of simulated differentially methylated regions and creating a HTML report using
renderReport(). The report is a bit simpler than the one in the example of
renderReport() because there is no p-value variable. The output report from this example is available at bumphunter-example.
In case the previous links don’t work, pre-compiled versions are available. Check the following links:
An example using DiffBind is showcased at DiffBind.html. This file shows the code for obtaining a set of differentially bounded sites and creating a HTML report using
renderReport() with custom code to create a MA plot and two PCA plots. This example also shows how to change the distribution plot templates to use histograms instead of density plots. The output report from this example is available at DiffBind-example and it uses
rmarkdown as the engine which since version 0.9.5 allows toggling of code.
This section uses different data sets as described in the
derfinder paper (bioRxiv preprint).
The reports can be viewed following these links:
Note that each report is around 40-50 MB in size and can take some time to load. These reports were generated using
knitrBootstrap as the engine prior to
Get R 3.2.x from CRAN as well as pandoc 1.12.3 or newer from here. Note that at the time of writing this page, some of the functionality of
regionReport is only available at Bioconductor-devel (BioC version 3.3) for which you’ll need R 3.3.x.
Once you have the correct version of R, you can install
regionReport directly from Bioconductor by using:
## Install regionReport source('http://bioconductor.org/biocLite.R') biocLite('regionReport')
That command should install all the dependencies for using
regionReport. This package does suggest several other packages, which you might not need to use. It will depend on the type of report that you are creating. If you wish to install them use:
## Here is the full list of suggested packages by regionReport source('http://bioconductor.org/biocLite.R') biocLite(c('BiocStyle', 'biovizBase', 'bumphunter', 'Cairo', 'derfinderPlot', 'devtools', 'DT', 'DESeq', 'edgeR', 'ggbio', 'ggplot2', 'grid', 'gridExtra', 'IRanges', 'mgcv', 'pasilla', 'pheatmap', 'RColorBrewer', 'TxDb.Hsapiens.UCSC.hg19.knownGene', 'whisker'))
Note that for the latest
knitrBootstrap templates you will have to use:
## Install latest knitrBootstrap from GitHub library('devtools') install_github('jimhester/knitrBootstrap')
Some of the examples require other packages, in which case you would need to install the following packages.
## DESeq2 example source("http://bioconductor.org/biocLite.R") biocLite('pasilla') ## edgeR example source("http://bioconductor.org/biocLite.R") biocLite(c('edgeR', 'DEFormats')) ## Bumphunter example, deps are part of the suggested list of packages source("http://bioconductor.org/biocLite.R") biocLite(c('bumphunter', 'GenomicRanges', 'biovizBase')) ## DiffBind example source("http://bioconductor.org/biocLite.R") biocLite(c('DiffBind', 'biovizBase', 'TxDb.Hsapiens.UCSC.hg19.knownGene', 'bumphunter')) ## derfinder examples. Should be installed after biocLite('regionReport') source("http://bioconductor.org/biocLite.R") biocLite('derfinder')
genomicRanges.R has simple code for determining how many unique packages depend, import or suggest
This page was last updated at 2016-05-11 13:42:06.