GDSArray
This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see GDSArray.
Representing GDS files as array-like objects
Bioconductor version: 3.11
GDS files are widely used to represent genotyping or sequence data. The GDSArray package implements the `GDSArray` class to represent nodes in GDS files in a matrix-like representation that allows easy manipulation (e.g., subsetting, mathematical transformation) in _R_. The data remains on disk until needed, so that very large files can be processed.
Author: Qian Liu [aut, cre], Martin Morgan [aut], Hervé Pagès [aut]
Maintainer: Qian Liu <qliu7 at buffalo.edu>
citation("GDSArray")):
Installation
To install this package, start R (version "4.0") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("GDSArray")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("GDSArray")| GDSArray: Representing GDS files as array-like objects | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DataRepresentation, GenotypingArray, Infrastructure, Sequencing, Software |
| Version | 1.8.0 |
| In Bioconductor since | BioC 3.7 (R-3.5) (6 years) |
| License | GPL-3 |
| Depends | R (>= 3.5), gdsfmt, methods, BiocGenerics, DelayedArray(>= 0.5.32) |
| Imports | tools, S4Vectors(>= 0.17.34), SNPRelate, SeqArray |
| System Requirements | |
| URL | https://github.com/Bioconductor/GDSArray |
| Bug Reports | https://github.com/Bioconductor/GDSArray/issues |
See More
| Suggests | testthat, knitr, BiocStyle, BiocManager |
| Linking To | |
| Enhances | |
| Depends On Me | VariantExperiment |
| Imports Me | CNVRanger |
| Suggests Me | DelayedDataFrame |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | GDSArray_1.8.0.tar.gz |
| Windows Binary | GDSArray_1.8.0.zip |
| macOS 10.13 (High Sierra) | GDSArray_1.8.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/GDSArray |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/GDSArray |
| Bioc Package Browser | https://code.bioconductor.org/browse/GDSArray/ |
| Package Short Url | https://bioconductor.org/packages/GDSArray/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.11 | Source Archive |