BioConductor

NarrowPeaks 1.24.0

Shape-based Analysis of Variation in ChIP-seq using Functional PCA

Released Jun 27, 2015 by Pedro Madrigal

This package can be loaded by Renjin but 1 out 5 tests failed.

Dependencies

IRanges 2.14.10 GenomeInfoDb 1.16.0 CSAR 1.32.0 ICSNP 1.1-1 fda 2.4.7 GenomicRanges 1.32.3 S4Vectors 0.18.2 BiocGenerics 0.26.0

The package applies a functional version of principal component analysis (FPCA) to: (1) Postprocess data in wiggle track format, commonly produced by generic ChIP-seq peak callers, by applying FPCA over a set of read-enriched regions (ChIP-seq peaks). This is done to study variability of the the peaks, or to shorten their genomic locations accounting for a given proportion of variation among the enrichment-score profiles. (2) Analyse differential variation between multiple ChIP-seq samples with replicates. The function 'narrowpeaksDiff' quantifies differences between the shapes, and uses Hotelling's T2 tests on the functional principal component scores to identify significant differences across conditions. An application of the package for Arabidopsis datasets is described in Mateos, Madrigal, et al. (2015) Genome Biology: 16:31.

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>NarrowPeaks</artifactId>
    <version>1.24.0-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>

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Renjin CLI

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

library('org.renjin.bioconductor:NarrowPeaks')

Test Results

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