Reporting of Custom Analysis
The goal of RoCA is to set up a paradigm of reproducible data analysis. It provides a framework for data analysts to conveniently re-run custom analysis using their own data and parameters. Each run will generates a self-contained output file folder and an index.html file as a summary report.
Download an example (unzip the file and open the index.html file to view report)
##### Table of contents - [How to use](#howto) * [Install R packages](#installR) * [Prepare for an analysis](#prepare) * [Generate a report](#report) - [Develop a template](#develop)
## How to use ### Install R packages
Use the code below to install default R packages. Please note that individual R Markdown templates might require extra packages. Read instruction of each template for details. Before start,
- make sure that base R version 3.2.3 or newer was installed through RStudio or R Console
- and open RStudio or R Console to start a new R session.
# install.packages(c('devtools', 'RCurl')); # if packages have not been installed
require(devtools);
require(RCurl);
devtools::install_github("zhezhangsh/RoCA/R"); # Install the RoCA package itself from GitHub
# Install default packages from Cran, GitHub, or Bioconductor, used by the RoCA package and Rmarkdown templates
# Note that individual Rmarkdown templates might require more packages
installed <- RoCA::InstallDependency(reinstall=FALSE) # Use reinstall=TRUE to force re-installing all packages
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Clone the whole RoCA GitHub repo
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Download and edit a YAML file
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Use the RoCA::CreateReport() function
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Use RStudio
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Use the knitr::knit() function
## Develop a template