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BEDMatrix

A matrix-like wrapper around PLINK .bed files

https://github.com/quantgen/bedmatrix

Science Score: 26.0%

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    Low similarity (12.1%) to scientific vocabulary

Keywords

bed cran genetics genomics plink plink2 r r-pkg
Last synced: 6 months ago · JSON representation

Repository

A matrix-like wrapper around PLINK .bed files

Basic Info
  • Host: GitHub
  • Owner: QuantGen
  • License: other
  • Language: C
  • Default Branch: master
  • Homepage:
  • Size: 1.84 MB
Statistics
  • Stars: 18
  • Watchers: 4
  • Forks: 2
  • Open Issues: 1
  • Releases: 0
Topics
bed cran genetics genomics plink plink2 r r-pkg
Created almost 11 years ago · Last pushed over 1 year ago
Metadata Files
Readme Changelog License

README.md

BEDMatrix

CRAN status <!-- badges: end -->

BEDMatrix is an R package that provides a matrix-like wrapper around .bed, one of the genotype/phenotype file formats of PLINK, the whole genome association analysis toolset. BEDMatrix objects are created in R by simply providing the path to a .bed file and once created, they behave similarly to regular matrices with the advantage that genotypes are retrieved on demand without loading the entire file into memory. This allows handling of very large files with limited use of memory.

This package is deliberately kept simple. For computational methods that use BEDMatrix check out the BGData package.

Example

This example uses a dummy .bed file that is bundled with this R package. It was generated using plink --dummy 500 1000 0.02 acgt --seed 4711 --out example with PLINK 1.90 beta 3.452.

To get the path to the example .bed file (system.file finds the full file names of files in packages and is only used to find the example data):

R path <- system.file("extdata", "example.bed", package = "BEDMatrix")

To wrap the example .bed file in a BEDMatrix object:

```R m <- BEDMatrix(path)

> Extracting number of samples and rownames from example.fam...

> Extracting number of variants and colnames from example.bim...

```

To get the dimensions of the BEDMatrix object:

```R dim(m)

> [1] 50 1000

```

To extract a subset of the BEDMatrix object:

```R m[1:3, 1:5]

> snp0A snp1C snp2G snp3G snp4_G

> per0_per0 0 1 1 1 0

> per1_per1 1 1 1 1 NA

> per2_per2 1 0 0 2 0

```

Installation

Install the stable version from CRAN:

R install.packages("BEDMatrix")

Alternatively, install the development version from GitHub:

```R

install.packages("remotes")

remotes::install_github("QuantGen/BEDMatrix") ```

Documentation

Further documentation can be found on RDocumentation.

Contributing

  • Issue Tracker: https://github.com/QuantGen/BEDMatrix/issues
  • Source Code: https://github.com/QuantGen/BEDMatrix

Owner

  • Name: QuantGen
  • Login: QuantGen
  • Kind: organization
  • Location: Michigan State University

GitHub Events

Total
  • Watch event: 1
Last Year
  • Watch event: 1

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 420
  • Total Committers: 2
  • Avg Commits per committer: 210.0
  • Development Distribution Score (DDS): 0.176
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Alexander Grueneberg a****g@g****m 346
Alexander Grueneberg g****t@a****o 74
Committer Domains (Top 20 + Academic)
agrueneberg.info: 1

Issues and Pull Requests

Last synced: 10 months ago

All Time
  • Total issues: 23
  • Total pull requests: 1
  • Average time to close issues: 5 months
  • Average time to close pull requests: about 20 hours
  • Total issue authors: 8
  • Total pull request authors: 1
  • Average comments per issue: 1.83
  • Average comments per pull request: 1.0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
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Top Authors
Issue Authors
  • agrueneberg (15)
  • rosieli5 (2)
  • lian0090 (1)
  • privefl (1)
  • DavidGO464 (1)
  • TabeaSchoeler (1)
  • zillurbmb51 (1)
  • Knox2020 (1)
Pull Request Authors
  • alexviiia (1)
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Packages

  • Total packages: 1
  • Total downloads:
    • cran 1,085 last-month
  • Total docker downloads: 38
  • Total dependent packages: 9
  • Total dependent repositories: 11
  • Total versions: 13
  • Total maintainers: 1
cran.r-project.org: BEDMatrix

Extract Genotypes from a PLINK .bed File

  • Versions: 13
  • Dependent Packages: 9
  • Dependent Repositories: 11
  • Downloads: 1,085 Last month
  • Docker Downloads: 38
Rankings
Dependent packages count: 5.7%
Dependent repos count: 8.7%
Average: 11.5%
Downloads: 12.2%
Stargazers count: 13.7%
Forks count: 17.1%
Maintainers (1)
cran@agrueneberg.info
Last synced: 6 months ago

Dependencies

DESCRIPTION cran
  • R >= 3.0.2 depends
  • crochet >= 2.3.0 imports
  • methods * imports
  • LinkedMatrix * suggests
  • data.table * suggests
  • tinytest * suggests