BioConductor

DMRScan 1.6.0

Detection of Differentially Methylated Regions

Released May 1, 2018 by Christian M Page

This package can be loaded by Renjin but 4 out 10 tests failed.

Dependencies

IRanges 2.14.10 GenomeInfoDb 1.16.0 Matrix 1.2-14 MASS 7.3-50 RcppRoll 0.2.2 GenomicRanges 1.32.3 mvtnorm 1.0-8

This package detects significant differentially methylated regions (for both qualitative and quantitative traits), using a scan statistic with underlying Poisson heuristics. The scan statistic will depend on a sequence of window sizes (# of CpGs within each window) and on a threshold for each window size. This threshold can be calculated by three different means: i) analytically using Siegmund et.al (2012) solution (preferred), ii) an important sampling as suggested by Zhang (2008), and a iii) full MCMC modeling of the data, choosing between a number of different options for modeling the dependency between each CpG.

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.bioconductor</groupId>
    <artifactId>DMRScan</artifactId>
    <version>1.6.0-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.bioconductor:DMRScan')

Test Results

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