BioConductor
gdsfmt 1.16.0
R Interface to CoreArray Genomic Data Structure (GDS) Files
Released Apr 15, 2018 by Xiuwen Zheng
This package provides a high-level R interface to CoreArray Genomic Data Structure (GDS) data files, which are portable across platforms with hierarchical structure to store multiple scalable array-oriented data sets with metadata information. It is suited for large-scale datasets, especially for data which are much larger than the available random-access memory. The gdsfmt package offers the efficient operations specifically designed for integers of less than 8 bits, since a diploid genotype, like single-nucleotide polymorphism (SNP), usually occupies fewer bits than a byte. Data compression and decompression are available with relatively efficient random access. It is also allowed to read a GDS file in parallel with multiple R processes supported by the package parallel.
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>gdsfmt</artifactId>
<version>1.16.0-b4</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.bioconductor:gdsfmt')
Test Results
This package was last tested against Renjin 0.9.2689 on Aug 26, 2018.
- add.gdsn-examples
- addfile.gdsn-examples
- addfolder.gdsn-examples
- append.gdsn-examples
- apply.gdsn-examples
- assign.gdsn-examples
- cache.gdsn-examples
- cleanup.gds-examples
- closefn.gds-examples
- clusterApply.gdsn-examples
- cnt.gdsn-examples
- compression.gdsn-examples
- copyto.gdsn-examples
- createfn.gds-examples
- delete.attr.gdsn-examples
- delete.gdsn-examples
- diagnosis.gds-examples
- digest.gdsn-examples
- gdsfmt-package-examples
- get.attr.gdsn-examples
- getfile.gdsn-examples
- getfolder.gdsn-examples
- index.gdsn-examples
- is.element.gdsn-examples
- lasterr.gds-examples
- ls.gdsn-examples
- moveto.gdsn-examples
- name.gdsn-examples
- objdesp.gdsn-examples
- openfn.gds-examples
- permdim.gdsn-examples
- print.gds.class-examples
- put.attr.gdsn-examples
- read.gdsn-examples
- readex.gdsn-examples
- readmode.gdsn-examples
- rename.gdsn-examples
- runTests
- setdim.gdsn-examples
- showfile.gds-examples
- summarize.gdsn-examples
- sync.gds-examples
- system.gds-examples
- write.gdsn-examples