README.md

RoCA

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)

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Quick links:

• Analysis templates & examples
• About R Markdown
• About YAML

Table of contents

• How to use
  • Install R packages
  • Prepare for an analysis
  • Generate a report
• Develop a template

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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/RoCAR"); # 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

Prepare for an analysis

1. Clone the whole RoCA GitHub repo

2. Download and edit a YAML file

Generate a report

1. Use the RoCA::CreateReport() function

2. Use RStudio

3. Use the knitr::knit() function

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Develop a template

R Markdown in a nutshell

The R Markdown/YAML pair

Required YAML fields

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