gdsfmt: R Interface to CoreArray Genomic Data Structure (GDS) files

This package provides a high-level R interface to CoreArray Genomic Data Structure (GDS) data files, which are portable across platforms and include 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 with less than 8 bits, since a single genetic/genomic variant, such like single-nucleotide polymorphism, usually occupies fewer bits than a byte. It is also allowed to read a GDS file in parallel with multiple R processes supported by the parallel package.

Version: 1.0.3
Depends: R (≥ 2.14.0)
Imports: methods, parallel
Suggests: RUnit
Published: 2014-03-19
Author: Xiuwen Zheng
Maintainer: Xiuwen Zheng <zhengx at>
License: LGPL-3
NeedsCompilation: yes
Citation: gdsfmt citation info
Materials: NEWS
In views: HighPerformanceComputing
CRAN checks: gdsfmt results


Reference manual: gdsfmt.pdf
Vignettes: A High-performance Computing Toolset for Big Data Analysis of Genome-Wide Variants
Package source: gdsfmt_1.0.3.tar.gz
MacOS X binary: gdsfmt_1.0.3.tgz
Windows binary:
Old sources: gdsfmt archive

Reverse dependencies:

Reverse depends: SNPRelate
Reverse imports: OmicKriging