mpbr

Population Genomics Analysis for Plasmodium falciparum

https://github.com/karim-mane/mpbr

Keywords

Repository

Population Genomics Analysis for Plasmodium falciparum

README.Rmd

---
output: github_document
---








```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse  = TRUE,
  comment   = "#>",
  fig.path  = "man/figures/README-",
  out.width = "100%"
)
```

# {{ packagename }} 


[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/license/mit/)
[![R-CMD-check](https://github.com/{{ gh_repo }}/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/{{ gh_repo }}/actions/workflows/R-CMD-check.yaml)
[![Codecov test coverage](https://codecov.io/gh/{{ gh_repo }}/branch/main/graph/badge.svg)](https://app.codecov.io/gh/{{ gh_repo }}?branch=main)
[![lifecycle-concept](https://raw.githubusercontent.com/reconverse/reconverse.github.io/master/images/badge-experimental.svg)](https://www.reconverse.org/lifecycle.html#concept) 


**{{ packagename }}** provides functions to perform population genomics analyses using genome-wide Single Nucleotide Polymorphisms (SNPs) from the malaria parasite _Plasmodium falciparum_.


**{{ packagename }}** is developed at the [Medical Research Council, The Gambia Unit at London School of Hygiene and Tropical Medicine](https://www.lshtm.ac.uk/research/units/mrc-gambia) as part of the [Malaria Population Genomics (MPB)](https://data.org/initiatives/epiverse/) initiative.

## Installation

You can install the development version of **{{ packagename }}** from
[GitHub](https://github.com/) with:

```{r eval=FALSE}
pak::pak("{{ gh_repo }}")
library(mpbr)
```

## Create the `SNPdata` object
The functions in the **{{ packagename }}** require a **SNPdata** object. This is
generated with the `get_snpdata()` function.   
The function's arguments and returned object are described in the vignette and the function documentation.

```{r "create_snpdata_object", echo = TRUE, eval = FALSE}
snpdata <- get_snpdata(
  vcf_file   = system.file("extdata", "Input_Data.vcf.gz", package = "mpbr"), 
  meta_file  = system.file("extdata", "SampleMetadata.RDS", package = "mpbr"), 
  output_dir = tempdir(), 
  gof        = system.file("extdata", "pf_gene_ontology.RDS", package = "mpbr"), 
  gff        = system.file("extdata", "PlasmoDB-56_Pfalciparum3D7.RDS",
                           package = "mpbr")
)
```

## Package Vignettes

The vignette of the **{{ packagename }}** contains detailed illustrations about the
use of each function. This can be accessed by typing the command below:

```{r "vignette", echo = TRUE, eval = FALSE}
# OPEN THE VIGNETTE WITHIN RSTUDIO
vignette("mpbr")

# OPEN THE VIGNETTE IN YOUR WEB BROWSER.
browseVignettes("mpbr")
```

## Development

### Lifecycle

This package is currently a *concept*, as defined by the [RECON software
lifecycle](https://www.reconverse.org/lifecycle.html). This means that essential
features and mechanisms are still being developed, and the package is not ready
for use outside of the development team.


### Contributions

Contributions are welcome via [pull requests](https://github.com/{{ gh_repo }}/pulls).

### Code of Conduct

Please note that the **{{ packagename }}** project is released with a 
[Contributor Code of Conduct](https://github.com/epiverse-trace/.github/blob/main/CODE_OF_CONDUCT.md).
By contributing to this project, you agree to abide by its terms.

## Citing this package

```{r message=FALSE, warning=FALSE}
citation("mpbr")
```

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Last synced: over 1 year ago