CRAN

GMAC 3.0

Genomic Mediation Analysis with Adaptive Confounding Adjustment

Released Dec 15, 2017 by Fan Yang

This package is available for Renjin and there are no known compatibility issues.

Performs genomic mediation analysis with adaptive confounding adjustment (GMAC) proposed by Yang et al. (2017) . It implements large scale mediation analysis and adaptively selects potential confounding variables to adjust for each mediation test from a pool of candidate confounders. The package is tailored for but not limited to genomic mediation analysis (e.g., cis-gene mediating trans-gene regulation pattern where an eQTL, its cis-linking gene transcript, and its trans-gene transcript play the roles as treatment, mediator and the outcome, respectively), restricting to scenarios with the presence of cis-association (i.e., treatment-mediator association) and random eQTL (i.e., treatment).

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>GMAC</artifactId>
    <version>3.0-b6</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:GMAC')

Test Results

This package was last tested against Renjin 0.9.2644 on Jun 1, 2018.

dat-examples

Source

View GitHub Mirror