CRAN

MiRKAT 1.0.1

Microbiome Regression-Based Kernel Association Test

Released Apr 25, 2018 by Ni Zhao

This package can be loaded by Renjin but 1 out 8 tests failed.

Dependencies

MASS 7.3-50 PearsonDS 1.1 survival 2.42-3 GUniFrac 1.1

Test for overall association between microbiome composition data with a continuous or dichotomous outcome via phylogenetic kernels. The phenotype can be univariate continuous or binary phenotypes (Zhao et al. (2015) ), survival outcomes (Plantinga et al. (2017) ), multivariate (Zhan et al. (2017) ) and structured phenotypes (Zhan et al. (2017) ). For all these effect, the microbiome community effect was modeled nonparametrically through a kernel function, which can incorporate the phylogenetic tree information.

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>MiRKAT</artifactId>
    <version>1.0.1-b2</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:MiRKAT')

Test Results

This package was last tested against Renjin 0.9.2644 on Jun 2, 2018.

Source

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