CRAN

detectRUNS 0.9.5

Detect Runs of Homozygosity and Runs of Heterozygosity in Diploid Genomes

Released Feb 6, 2018 by Filippo Biscarini

This package can be loaded by Renjin but 17 out 46 tests failed.

Dependencies

itertools 0.1-3 plyr 1.8.4 Rcpp data.table 1.10.4-3 iterators 1.0.9 ggplot2 2.2.1 reshape2 1.4.3 gridExtra 2.3

Detection of runs of homozygosity and of heterozygosity in diploid genomes using two methods: sliding windows (Purcell et al (2007) ) and consecutive runs (Marras et al (2015) ).

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>detectRUNS</artifactId>
    <version>0.9.5-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>

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Renjin CLI

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

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

Test Results

This package was last tested against Renjin 0.9.2594 on Feb 8, 2018.

Source

R
C++

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