CRAN
xseq 0.2.1
Assessing Functional Impact on Gene Expression of Mutations in Cancer
Released Sep 11, 2015 by Jiarui Ding
Dependencies
impute 1.42.0 gptk 1.08 e1071 1.6-7 preprocessCore 1.30.0 sfsmisc 1.0-28 RColorBrewer 1.1-2
A hierarchical Bayesian approach to assess functional impact of mutations on gene expression in cancer. Given a patient-gene matrix encoding the presence/absence of a mutation, a patient-gene expression matrix encoding continuous value expression data, and a graph structure encoding whether two genes are known to be functionally related, xseq outputs: a) the probability that a recurrently mutated gene g influences gene expression across the population of patients; and b) the probability that an individual mutation in gene g in an individual patient m influences expression within that patient.
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>xseq</artifactId>
<version>0.2.1-b51</version>
</dependency>
</dependencies>
<repositories>
<repository>
<id>bedatadriven</id>
<name>bedatadriven public repo</name>
<url>https://nexus.bedatadriven.com/content/groups/public/</url>
</repository>
</repositories>
Renjin CLI
If you're using Renjin from the command line, you load this library by invoking:
library('org.renjin.cran:xseq')
Test Results
This package was last tested against Renjin 0.8.2500 on Oct 28, 2017.