Genetic association testing using the GENESIS R/Bioconductor package

The Genomic Data Storage (GDS) format provides efficient storage and retrieval of genotypes measured by microarrays and sequencing. We developed GENESIS to perform various single- and aggregate-variant association tests using genotype data stored in GDS format. GENESIS implements highly flexible mix...

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Bibliographic Details
Published in:Bioinformatics (Oxford, England) Vol. 35; no. 24; pp. 5346 - 5348
Main Authors: Gogarten, Stephanie M, Sofer, Tamar, Chen, Han, Yu, Chaoyu, Brody, Jennifer A, Thornton, Timothy A, Rice, Kenneth M, Conomos, Matthew P
Format: Journal Article
Language:English
Published: England Oxford University Press 15.12.2019
Subjects:
Applications Notes
Genetic Testing
Genome
Genomics
Sequence Analysis
Software
ISSN:1367-4803, 1367-4811, 1367-4811
Online Access:Get full text
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Summary:The Genomic Data Storage (GDS) format provides efficient storage and retrieval of genotypes measured by microarrays and sequencing. We developed GENESIS to perform various single- and aggregate-variant association tests using genotype data stored in GDS format. GENESIS implements highly flexible mixed models, allowing for different link functions, multiple variance components and phenotypic heteroskedasticity. GENESIS integrates cohesively with other R/Bioconductor packages to build a complete genomic analysis workflow entirely within the R environment. https://bioconductor.org/packages/GENESIS; vignettes included. Supplementary data are available at Bioinformatics online.
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ISSN:1367-4803
1367-4811
1367-4811
DOI:10.1093/bioinformatics/btz567