RT Journal Article
SR Electronic
T1 plyranges: A grammar of genomic data transformation
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 327841
DO 10.1101/327841
A1 Stuart Lee
A1 Di Cook
A1 Michael Lawrence
YR 2018
UL http://biorxiv.org/content/early/2018/05/23/327841.abstract
AB The Bioconductor project has created many useful data abstractions for analysing high-throughput genomics experiments. However, there is a cognitive load placed on a user in learning a data abstraction and understanding its appropriate use. Through-out a standard workflow, a user must navigate and know many of these abstractions to perform an genomic analysis task, when a single data abstraction, a GRanges object will suffice. The GRanges class naturally represent genomic intervals and their associated measurements. By recognising that the GRanges class follows ‘tidy’ data principles we have created a grammar of genomic data transformation. The grammar defines verbs for performing actions on and between genomic interval data. It provides a principled way of performing common genomic data analysis tasks through a coherent interface to existing Bioconductor infrastructure, resulting in human readable analysis workflows. We have implemented this grammar as a Bioconductor/R package called plyranges.