README.md

In btmonier/vidger-nd: Create rapid visualizations of RNAseq data in R

ViDGER-nd

Overview

Visualization of Differential Gene Expression using R

Note: this is the non-developmental version of ViDGER. This version of ViDGER requires you to have an R version >= 3.4.

Installation

The easiest way to obtain this package is to install devtools and pull the package contents directly from GitHub.

if (!require("devtools")) install.packages("devtools")
devtools::install_github("btmonier/vidger-nd")

New Functions

• vsScatterPlot()
• vsScatterMatrix()
• vsBoxplot()
• vsDEGMatrix()
• vsVolcano()
• vsVolcanoMatrix()
• vsMAPlot()
• vsMAMatrix()
• vsFourWay()

Package Dependencies

This package requires a few additional packages to work properly. Make sure the following packages are installed and loaded into your R directory. The current version of the package automatically installs and loads these if not found in your R directory:

• ggplot2 for main visualizations
• dplyr for data munging
• tidyr for additional data munging
• GGally for matrix visualizations

Loading test data

I have loaded three objects from three seperate analysis types:

• df.cuff A cuffdiff output file.
• df.deseq A DESeq2 object class.
• df.edger An edgeR object class.

To load these data sets, use the following command:

data("<object-type>")

...where <object-type> is one of the previously mentioned data sets.

Getting help

For additional information on these functions, please see the given documentation in the vidger package by adding the ? help operator before any of the given functions in this package or by using the help() function.

btmonier/vidger-nd documentation built on May 14, 2019, 12:44 p.m.