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cgmisc

R build status Coverage status

Overview

cgmisc is a R package that enables enhanced data analysis and visualisation of results from GWAS. The package contains several utilities and modules that complement and enhance the functionality of existing softwares. It also provides several tools for advanced visualisation of genomic data and utilises the power of the R language to aid in preparation of publication-quality figures. Some of the package functions are specific for the domestic dog (Canis familiaris) data.

Releases

Beginning from version 2.9.11, we are no longer using releases system. Instead, we maintain cgmisc in the CD/CI manner. From time to time, major versions will be frozen and available as source packages. Otherwise, track commit messages to know what has changed.

Docker container

For you who are familiar with Docker, there is a cgmisc container available from the DockerHub, so that you can just:
docker pull quiestrho/cgmisc:latest

Pre-requisites

cgmisc enchances functionalities of GenABEL package which is, unfortunately, no longer supported. Thus you will need to install it manualy from source available on CRAN Package Archives:

  • install.packages("https://cran.r-project.org/src/contrib/Archive/GenABEL.data/GenABEL.data_1.0.0.tar.gz", type='source', repos=NULL)

  • install.packages("https://cran.r-project.org/src/contrib/Archive/GenABEL/GenABEL_1.8-0.tar.gz", type='source', repos=NULL)

In addition, some more packages are required, but they should be installed automatically. We recommend to use an excellent renv package to recreate optimal environment for cgmisc installation. First, retrieve the renv.lock file:
wget https://raw.githubusercontent.com/cgmisc-team/cgmisc/master/renv.lock
and put it in your project directory. Next, type this in R:

install.packages(renv)
library(renv)
renv::init()

Installation

Otherwise, we recommend installing cgmisc by using: devtools::install_github('cgmisc-team/cgmisc')

To install using the tarball, open a terminal and type: R CMD INSTALL cgmisc_[version].tar.gz

How to cite cgmisc

Kierczak M, Jablonska J, Forsberg SKG, Bianchi M, Tengvall K, Pettersson M, Scholz V, Meadows JRS, Jern P, Carlborg O Lindblad-Toh K. cgmisc: enhanced genome-wide association analyses and visualization. Bioinformatics. Oxford University Press; 2015;31: 3830-3831. doi:10.1093/bioinformatics/btv426

Selected publications that used cgmisc

Here we list some publications where cgmisc has been helpful: