CRAN

OmicKriging 1.4.0

Poly-Omic Prediction of Complex TRaits

Released Mar 8, 2016 by Hae Kyung Im

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

Dependencies

doParallel 1.0.11 foreach 1.4.4 irlba 2.3.2 ROCR 1.0-7

It provides functions to generate a correlation matrix from a genetic dataset and to use this matrix to predict the phenotype of an individual by using the phenotypes of the remaining individuals through kriging. Kriging is a geostatistical method for optimal prediction or best unbiased linear prediction. It consists of predicting the value of a variable at an unobserved location as a weighted sum of the variable at observed locations. Intuitively, it works as a reverse linear regression: instead of computing correlation (univariate regression coefficients are simply scaled correlation) between a dependent variable Y and independent variables X, it uses known correlation between X and Y to predict Y.

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>OmicKriging</artifactId>
    <version>1.4.0-b31</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:OmicKriging')

Test Results

This package was last tested against Renjin 0.9.2687 on Aug 25, 2018.

Source

R

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Release History