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Genome Biol. 2019 Jan 4;20(1):4. doi: 10.1186/s13059-018-1597-8.

plyranges: a grammar of genomic data transformation.

Author information

1
Department of Econometrics and Business Statistics, Monash University, Clayton, Australia.
2
Molecular Medicine Division, Walter and Eliza Hall Institute, Parkville, Australia.
3
Bioinformatics and Computational Biology, Genentech Research and Early Development, South San Francisco, USA. michafla@gene.com.

Abstract

Bioconductor is a widely used R-based platform for genomics, but its host of complex genomic data structures places a cognitive burden on the user. For most tasks, the GRanges object would suffice, but there are gaps in the API that prevent its general use. By recognizing that the GRanges class follows "tidy" data principles, we create a grammar of genomic data transformation, defining verbs for performing actions on and between genomic interval data and providing a way of performing common data analysis tasks through a coherent interface to existing Bioconductor infrastructure. We implement this grammar as a Bioconductor/R package called plyranges.

KEYWORDS:

Bioconductor; Data analysis; Genomes; Grammar

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