mpbr

mpbr provides functions to perform population genomics analyses using genome-wide Single Nucleotide Polymorphisms (SNPs) from the malaria parasite Plasmodium falciparum.

mpbr is developed at the Medical Research Council, The Gambia Unit at London School of Hygiene and Tropical Medicine as part of the Malaria Population Genomics (MPB) initiative.

Installation

You can install the development version of mpbr from GitHub with:

pak::pak("Karim-Mane/mpbr")
library(mpbr)

Create the SNPdata object

The functions in the mpbr 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.

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 mpbr contains detailed illustrations about the use of each function. This can be accessed by typing the command below:

# 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. 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.

Code of Conduct

Please note that the mpbr project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.

Citing this package

citation("mpbr")
#> To cite package 'mpbr' in publications use:
#> 
#>   Mané K, Ngwa A, Jeffries D (2024). _mpbr: Population Genomics
#>   Analysis for Plasmodium falciparum_.
#>   <https://Karim-Mane.github.io/mpbr/,https://github.com/Karim-Mane/mpbr/>.
#> 
#> A BibTeX entry for LaTeX users is
#> 
#>   @Manual{,
#>     title = {mpbr: Population Genomics Analysis for Plasmodium falciparum},
#>     author = {Karim Mané and Alfred Amambua Ngwa and David Jeffries},
#>     year = {2024},
#>     url = {https://Karim-Mane.github.io/mpbr/,
#> https://github.com/Karim-Mane/mpbr/},
#>   }