FindMyFriends standard base class for pangenomic data

Description

This virtual class is the superclass of the standard pangenome classes in FindMyFriends. It defines storage for everything except gene information, which is delegated to its subclasses.

Details

As gene storage is not defined in this class the following methods must be defined by subclasses:

genes(object, split, subset)

Return the underlying sequences. If split is missing return an XStringSet, otherwise return an XStringSetList. split can be either 'group', 'organism' or 'paralogue' and should group the sequences accordingly. Subset should behave as if it was added as '[]' to the results but allow you to avoid reading everything into memory if not needed.

geneNames(object)

Return a character vector with the name of each gene.

geneNames<-(object, value)

Set the name of each gene.

geneWidth(object)

Return an integer vector with the length (in residues) of each gene.

removeGene(object, name, organism, group, ind)

Should only be implemented for signature: c(yourClass, 'missing', 'missing', 'missing', 'integer') Remove the genes at the given indexes and return the object.

Slots

seqToOrg

An integer vector that reference all genes to a specific organism.

seqToGeneGroup

An integer vector that references all genes to a specific gene group.

groupInfo

A data.frame storing metadata information about gene groups.

orgInfo

A data.frame storing metadata information about organisms

See Also

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

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