https://github.com/oumarkme/geno2r

R package for reading genotype data
https://github.com/oumarkme/geno2r

Last synced: about 2 months ago
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R package for reading genotype data

• Host: GitHub
• URL: https://github.com/oumarkme/geno2r
• Owner: oumarkme
• License: other
• Created: 2023-11-10T13:31:53.000Z (about 1 year ago)
• Default Branch: main
• Last Pushed: 2024-02-02T13:25:43.000Z (12 months ago)
• Last Synced: 2024-02-03T14:44:14.025Z (12 months ago)
• Language: R
• Homepage: http://www.oumark.net/geno2r/
• Size: 10.5 MB
• Stars: 0
• Watchers: 1
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
# geno2r

[![R-CMD-check](https://github.com/oumarkme/geno2r/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/oumarkme/geno2r/actions/workflows/R-CMD-check.yaml) [![Lifecycle: stable](https://img.shields.io/badge/lifecycle-stable-brightgreen.svg)](https://lifecycle.r-lib.org/articles/stages.html#stable)

The goal of geno2r is to easily import genotype data from various formats into R.

[HTSlib](https://github.com/samtools/htslib/) is wrapped and imported by [Rsamtools](https://bioconductor.org/packages/release/bioc/html/Rsamtools.html), to enhance the VCF reading speed. In order to efficiently read a VCF file, it should be compressed with [bgzip](https://www.htslib.org/doc/bgzip.html) and indexed with [tabix](https://www.htslib.org/doc/tabix.html).

## Installation

You can install the most recent version of geno2r from GitHub with:

``` r

#install.packages("remotes")

remotes::install_github("oumarkme/geno2r", force=TRUE)

```

## Example

This is a basic example which shows you how to read VCF data to R with [`read_vcf()`](reference/read_vcf.html):

``` r

library(geno2r)

read_vcf(file = "human.vcf.gz", range="22:49379357")   # or

read_vcf(file = "human.vcf.gz", range="22:49379357-49379357")   # or

read_vcf(file = "human.vcf.gz", range=NULL)

```

## Example data

You can find an example VCF file on [Github](https://github.com/oumarkme/geno2r/tree/main/vcf_data_example).