gdsfmt
Bioc currentR Interface to CoreArray Genomic Data Structure (GDS) Files
Release Lineage
Entered 3.0 · Oct 14, 2014
Current · Requires R 4.6
Description
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.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
1872 46 exported
Complexity
4.4 avg / 39 max
Call network
1872 nodes / 1292 edges
Test coverage is not measured for Bioconductor packages; nodes fall back to a neutral fill.
Call graph
Open call graph →Lowest coverage
Per-function coverage is not measured for this package yet.
Code
Structure
Lines of code
80,716
Files
172
Compiled share
92.5%
Has compiled src
Yes
Language breakdown
API
Exported functions
46
Internal functions
21
Testing
Has tests
Yes
Test-to-code ratio
0.00
testthat edition
–
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
–
Unsafe pattern score
0
Dep constraint coverage
0%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
2.15.0
System requirements
–
C++ standard
–
License
LGPL-3
License flags
SPDX valid, OSI approved
History
Versions
24
First release
2015-01-16
Latest release
2026-06-24
Avg cadence
189 days
Cold removal rate
–
Dep drift
0
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 48includes a package overview page
- Examples that run
- 100%46 run in a plain check
- Exported functions with examples
- 100%
- Documented parameters
- 100%
- Return-value docs
- 100%
- Help pages citing references
- 6%
Repository practices
3 development-tooling and community-health practices detected across 2 families in the upstream repository
Checks run against github.com/zhengxwen/gdsfmt on 2026-10-22.
The R CMD check workflow runs on Linux and macOS
Topics
Depended on by (24)
Show all 26 packagesHide all 26 packages
Bioconductor (19)
CRAN (5)
Suggested by (2)
People (from the free-text Author field)
- Xiuwen Zheng author maintainer
- Stephanie Gogarten contributor
- Jean-loup Gailly
-
Mark Adler
contributor
for the included zlib sources
-
Yann Collet
contributor
for the included LZ4 sources
-
xz contributors
contributor
for the included liblzma sources
Cite
Cite this package
Run in R for the authors' entry:
citation("gdsfmt")The package provides a citation file, so citation() returns the authors' own entry.
It points to 10.1093/bioinformatics/bts606, 10.1093/bioinformatics/btx145.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-24, which the citation names so these numbers can be found later. More on citing and the projects behind them.