MAGNAMWAR: An R Package for Genome-Wide Association Studies of Bacterial Orthologs

Bioinformatics. 2018 Jun 1;34(11):1951-1952. doi: 10.1093/bioinformatics/bty001.

Abstract

Summary: Here we report on an R package for genome-wide association studies of orthologous genes in bacteria. Before using the software, orthologs from bacterial genomes or metagenomes are defined using local or online implementations of OrthoMCL. These presence-absence patterns are statistically associated with variation in user-collected phenotypes using the Mono-Associated GNotobiotic Animals Metagenome-Wide Association R package (MAGNAMWAR). Genotype-phenotype associations can be performed with several different statistical tests based on the type and distribution of the data.

Availability and implementation: MAGNAMWAR is available on CRAN.

Contact: john_chaston@byu.edu.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Bacteria / genetics
  • Bacteria / metabolism*
  • Bacterial Proteins / genetics*
  • Genome, Bacterial*
  • Genome-Wide Association Study / methods*
  • Metagenome
  • Polymorphism, Single Nucleotide
  • Software*

Substances

  • Bacterial Proteins