zhengxwen/gdsfmt: R Interface to CoreArray Genomic Data Structure (GDS) Files
Provides a high-level R interface to CoreArray Genomic Data Structure (GDS) data files. GDS is 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.
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Package details |
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| Author | Xiuwen Zheng [aut, cre] (<https://orcid.org/0000-0002-1390-0708>), Stephanie Gogarten [ctb], Jean-loup Gailly and Mark Adler [ctb] (for the included zlib sources), Yann Collet [ctb] (for the included LZ4 sources), xz contributors [ctb] (for the included liblzma sources) |
| Bioconductor views | DataImport Infrastructure |
| Maintainer | Xiuwen Zheng <zhengx@u.washington.edu> |
| License | LGPL-3 |
| Version | 1.42.0 |
| URL | https://github.com/zhengxwen/gdsfmt |
| Package repository | View on GitHub |
| Installation |
Install the latest version of this package by entering the following in R:
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