CRAN

vcfR 1.8.0

Manipulate and Visualize VCF Data

Released Apr 17, 2018 by Brian J. Knaus

This package can be loaded by Renjin but 12 out 107 tests failed.

Dependencies

vegan 2.5-1 ape 5.1 magrittr 1.5 Rcpp memuse 4.0-0 stringr 1.3.0 viridisLite 0.3.0 pinfsc50 1.1.0 dplyr 0.7.4 tibble 1.4.2

Facilitates easy manipulation of variant call format (VCF) data. Functions are provided to rapidly read from and write to VCF files. Once VCF data is read into R a parser function extracts matrices of data. This information can then be used for quality control or other purposes. Additional functions provide visualization of genomic data. Once processing is complete data may be written to a VCF file (*.vcf.gz). It also may be converted into other popular R objects (e.g., genlight, DNAbin). VcfR provides a link between VCF data and familiar R software.

Installation

Maven

This package can be included as a dependency from a Java or Scala project by including the following your project's pom.xml file. Read more about embedding Renjin in JVM-based projects.

<dependencies>
  <dependency>
    <groupId>org.renjin.cran</groupId>
    <artifactId>vcfR</artifactId>
    <version>1.8.0-b1</version>
  </dependency>
</dependencies>
<repositories>
  <repository>
    <id>bedatadriven</id>
    <name>bedatadriven public repo</name>
    <url>https://nexus.bedatadriven.com/content/groups/public/</url>
  </repository>
</repositories>

View build log

Renjin CLI

If you're using Renjin from the command line, you load this library by invoking:

library('org.renjin.cran:vcfR')

Test Results

This package was last tested against Renjin 0.9.2635 on Apr 26, 2018.

Source

C++

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