pgVirtualLoc-class: Superclass for gene location aware pangenome

Description Details See Also

Description

This virtual class should be subclassed by all classes that include chromosomal position of the genes (along with subclassing pgVirtual). The class itself is an empty shell that only takes care of dispatching and checking the promises of subclasses are held.

Details

Subclasses of pgVirtualLoc must implement the following methods:

geneLocation(object)

Return a data.frame with a row for each gene, describing the chromosomal position of the gene. The data.frame must contain the columns 'contig', 'start', 'end' and 'strand'. Contig is self-explanatory, start and end is the respective start and end positions on the contig (start must be lower than end) and strand defines the coding direction as -1 or 1.

See Also

Other Pangenome_classes: pgFull-class, pgFullLoc-class, pgInMem-class, pgInMemLoc-class, pgLM-class, pgLMLoc-class, pgSlim-class, pgSlimLoc-class, pgVirtual-class



Search within the FindMyFriends package
Search all R packages, documentation and source code

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.