CRAN
MsatAllele 1.05
Visualizes the scoring and binning of microsatellite fragment sizes
Released Nov 20, 2013 by Filipe Alberto
The package contains functions to: 1) load ah files from Strand software and build a R data base; 2) plot different graphical displays of the fragment sizes obtained for each locus and their bins; 3) interact with graphs to sort the data base for a given locus and range, allowing to easily trace back a particular group of samples to its original Strand file; bin fragment size data into population genetics files. 4) From version 1.04 on, the user can set manually bin limits and write files combining the manual and automatic methods to bin alleles.
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>MsatAllele</artifactId>
<version>1.05-b259</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:MsatAllele')
Test Results
This package was last tested against Renjin 0.9.2709 on Nov 8, 2018.
- AlleleCum-examples
- AlleleHist-examples
- BinStat-examples
- DBZn-examples
- DBase-examples
- InputFile-examples
- MsatAllele-package-examples
- OrderByLocus-examples
- STRandOUT-examples
- bin.limits-examples
- get.allele-examples
- getpoints-examples
- mark.bins-examples
- read.ah.file-examples
- read.frag.sizes-examples
- restrict.hist-examples
- subdataBase-examples
- transDB-examples
- write.PG.file.all-examples
- write.PG.file.loc-examples
- write.data-examples