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, like single-nucleotide polymorphism, usually occupies fewer bits than a byte. Data compression and decompression are also supported with relatively efficient random access. It is allowed to read a GDS file in parallel with multiple R processes supported by the parallel package.
Package details |
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Author | Xiuwen Zheng [aut, cre], Jean-loup Gailly [ctb] (zlib library), Mark Adler [ctb] (zlib library), Yann Collet [ctb] (LZ4 library) |
Maintainer | Xiuwen Zheng <zhengx@u.washington.edu> |
License | LGPL-3 |
Version | 1.1.3 |
URL | http://corearray.sourceforge.net/ http://github.com/zhengxwen/gdsfmt |
Package repository | View on R-Forge |
Installation |
Install the latest version of this package by entering the following in R:
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