CRAN

mrMLM 3.0

Multi-Locus Random-SNP-Effect Mixed Linear Model Tools for Genome-Wide Association Study

Released Mar 12, 2018 by Yuanming Zhang

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

Dependencies

ggplot2 2.2.1 qqman 0.1.4 sampling 2.8 data.table 1.10.4-3 doParallel 1.0.11 ncvreg 3.9-1 openxlsx 4.0.17 stringr 1.3.0 MASS 7.3-49 coin 1.2-2 foreach 1.4.4 lars 1.2

Conduct multi-locus genome-wide association study under the framework of random-SNP-effect mixed linear model (mrMLM). First, each marker on the genome is scanned. Bonferroni correction is replaced by a less stringent selection criterion for significant test. Then, all the markers that are potentially associated with the trait are included in a multi-locus model, their effects are estimated by empirical Bayes and true QTN are identified by likelihood ratio test.

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>mrMLM</artifactId>
    <version>3.0-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:mrMLM')

Test Results

This package was last tested against Renjin 0.9.2615 on Mar 27, 2018.

mrMLM-examples

Source

View GitHub Mirror