radiator

RADseq Data Exploration, Manipulation and Visualization using R

thierrygosselin
45
18
R

output: github_document

description <- readLines("DESCRIPTION")
rvers <- stringr::str_match(grep("R \\(", description, value = TRUE), "[0-9]{1,4}\\.[0-9]{1,4}\\.[0-9]{1,4}")[1,1]
version <- gsub(" ", "", gsub("Version:", "", grep("Version:", description, value = TRUE)))

lifecycle
Project Status: Active – The project has reached a stable, usable state and is being actively developed.
![packageversion](https://img.shields.io/badge/Package%20version-r version-orange.svg)
![Last-changedate](https://img.shields.io/badge/last%20change-r gsub('-', '--', Sys.Date())-brightgreen.svg)
R-CMD-check
DOI

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "README-"
)

radiator: an R package for RADseq Data Exploration, Manipulation and Visualization

Most genomic analysis look for patterns and trends with various statistics.
Bias, noise and outliers can have bounded influence on estimators and interfere
with polymorphism discovery. Avoid bad data exploration and control the impact
of filters on your downstream genetic analysis. Use radiator to: import, explore,
manipulate, visualize, filter, impute and export your GBS/RADseq data.

radiator is designed and optimized for fast computations of diploid data
using Genomic Data Structure GDS file
format and data science packages in
tidyverse. radiator handles VCF files with millions of
SNPs and files of several GB.

Installation

To try out the dev version of radiator, copy/paste the code below:

if (!require("devtools")) install.packages("devtools")
devtools::install_github("thierrygosselin/radiator")
library(radiator)

Note

Some Windows OS and Linux OS recently experienced some problems during installations,
linked to CRAN & Bioconductor tango problems:

  • If you’re experiencing problems with radiator installation see
    troubleshooting section
    and try the lines below.

  • Verify that installing radiator also installed the
    Bioconductor
    packages: gdsfmt and
    SeqArray with version >= 1.28.1.

devtools::package_info(pkgs = "SeqArray") # to verify version

# If manually installing SeqArray is necessary
install.packages("BiocManager")
BiocManager::install("SeqArray")

Web site with additional info: https://thierrygosselin.github.io/radiator/

Life cycle

radiator is maturing, but in order to make the package better, changes are
inevitable. Experimental functions will change, argument names will change.
Your codes and workflows might break from time to time until radiator is stable.
Consequently, depending on your tolerance to change, radiator might not be for you.
Avoid using radiator if you suffer from the Semmelweis reflex.
Philosophy, major changes and deprecated functions/arguments are documented in
life cycle section of functions.