CRAN

AssocAFC 1.0.2

Allele Frequency Comparison

Released May 5, 2018 by Khalid B. Kunji

This package can be loaded by Renjin but 1 out 9 tests failed.

Dependencies

CompQuadForm 1.4.3

When doing association analysis one does not always have the genotypes for the control population. In such cases it may be necessary to fall back on frequency based tests using well known sources for the frequencies in the control population, for instance, from the 1000 Genomes Project. The Allele Frequency Comparison ('AssocAFC') package performs multiple rare variant association analyses in both population and family-based GWAS (Genome-Wide Association Study) designs. It includes three score tests that are based on the difference of the sum of allele frequencies between cases and controls. Two of these tests, Wcorrected() and Wqls(), are collapsing-based tests and suffer from having protective and risk variants. The third test, afcSKAT(), is a score test that overcomes the mix of SNP (Single-Nucleotide Polymorphism) effect directions. For more details see Saad M and Wijsman EM (2017) .

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>AssocAFC</artifactId>
    <version>1.0.2-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>

View build log

Renjin CLI

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

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

Test Results

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

Source

R

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Release History