CRAN

alleHap 0.9.2

Allele Imputation and Haplotype Reconstruction from Pedigree Databases

Released Oct 5, 2015 by Nathan Medina-Rodriguez and Angelo Santana

This package can be loaded by Renjin but all tests failed.

Dependencies

abind 1.4-3

Simulation of alphanumeric alleles, imputation of genetic missing data and reconstruction of non-recombinant haplotypes from pedigree databases in a deterministic way. Allelic simulations can be implemented taking into account many different factors (such as number of families, markers, alleles per marker, probability and proportion of missing genotypes, recombination rate, etc). Genotype imputation can be used either simulated datasets or loaded databases (in .ped file biallelic format). Haplotype reconstruction can be performed even with missing data because of alleHap, firstly imputes the genotypes. All this considering that each member (due to meiosis) should unequivocally have two alleles, one inherited from each parent.

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>alleHap</artifactId>
    <version>0.9.2-b18</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:alleHap')

Test Results

This package was last tested against Renjin 0.8.2346 on Mar 18, 2017.

Source

R

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Release History