GDSArray
This is the development version of GDSArray; for the stable release version, see GDSArray.
Representing GDS files as array-like objects
Bioconductor version: Development (3.24)
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], Martin Morgan [aut], Hervé Pagès [aut], Xiuwen Zheng [aut, cre]
Maintainer: Xiuwen Zheng <zhengx at u.washington.edu>
citation("GDSArray")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
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 | 1.33.0 |
| In Bioconductor since | BioC 3.7 (R-3.5) (8.5 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, markdown, rmarkdown, BiocStyle, BiocManager |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | CNVRanger, VariantExperiment |
| 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_1.33.0.tar.gz |
| Windows Binary (x86_64) | GDSArray_1.33.0.zip |
| macOS Binary (big-sur-x86_64) | GDSArray_1.33.0.tgz |
| macOS Binary (sonoma-arm64) | GDSArray_1.33.0.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 |