Work

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

Year: 2018

Type: article

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: [email protected].

Source: Bioinformatics

DOI: 10.1093/bioinformatics/bty001

Authors: Corinne E Sexton, Hayden Z Smith, Peter D Newell, Angela E Douglas, John M Chaston

Institutions: Brigham Young University, State University of New York at Oswego, Cornell University

Language: English

Topic: Genomics and Phylogenetic Studies

Subfield: Molecular Biology

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

Open Access status: green

Funders: Foundation for the National Institutes of Health, Brigham Young University, National Institute of General Medical Sciences

Awards: Investigation of microbial factors required for integrated functions of the Droso, G5884655920, Integrating the Metabolic Function and Population Dynamics of Gut Microbiota for Host Nutritional Health