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.
| Author | Xiuwen Zheng |
| Maintainer | Xiuwen Zheng |
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("gdsfmt")
| CoreArrayTutorial.pdf | R Script | |
|---|---|---|
| Reference Manual |
| biocViews | |
|---|---|
| Depends |
R
|
| Imports |
methods
,
parallel
|
| Suggests |
RUnit
|
| System Requirements | |
| License | LGPL-3 |
| URL | http://corearray.sourceforge.net/, http://github.com/zhengxwen/CoreArray/ |
| Depends On Me |
SNPRelate
|
| Imports Me | |
| Suggests Me |
| Package source | gdsfmt_1.0.4.tar.gz |
|---|---|
| Windows 32-bit binary | gdsfmt_1.0.4.zip |
| Windows 64-bit binary | gdsfmt_1.0.4.zip |
| MacOS X 10.5 (Leopard) binary | Not Available |