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

MAGNAMWAR: an R package for genome-wide association studies of bacterial orthologs.

Author information

1
Department of Biology, Brigham Young University, Provo, UT 84602, USA.
2
Department of Biological Sciences, SUNY Oswego, Oswego, NY 13126, USA.
3
Department of Entomology and Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA.
4
Department of Plant & Wildlife Sciences, Brigham Young University, Provo, UT 84602, USA.

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.

PMID:
29342236
PMCID:
PMC5972563
[Available on 2019-06-01]
DOI:
10.1093/bioinformatics/bty001

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