internalMergePangenomes: Merge information from two pangenomes

In thomasp85/FindMyFriends: Microbial Comparative Genomics in R

Description

This method is for internal use only and should not be called directly. Use addGenomes instead. It is required for subclasses of pgVirtual.

Usage

mergePangenomes(pg1, pg2, ...)

## S4 method for signature 'pgInMem,pgInMem'
mergePangenomes(pg1, pg2, geneGrouping,
  groupInfo, ...)

## S4 method for signature 'pgLM,pgLM'
mergePangenomes(pg1, pg2, geneGrouping, groupInfo,
  ...)

## S4 method for signature 'pgLMLoc,pgLMLoc'
mergePangenomes(pg1, pg2, geneGrouping,
  groupInfo)

## S4 method for signature 'pgFull,pgFull'
mergePangenomes(pg1, pg2, geneGrouping,
  groupInfo, ...)

## S4 method for signature 'pgFullLoc,pgFullLoc'
mergePangenomes(pg1, pg2, geneGrouping,
  groupInfo)

## S4 method for signature 'pgSlimLoc,pgSlimLoc'
mergePangenomes(pg1, pg2, geneGrouping,
  groupInfo)

Arguments

pg1	A pgVirtual subclass
pg2	An object of the same class as pg1
...	Parameters to be passed on
geneGrouping	The grouping of the genees in the merged pangenome. Equivalent to calling seqToGeneGroup on the new object
groupInfo	The metadata on the gene groups in the merged pangenome. Equivalent to calling groupInfo on the new object

Value

An object of the same class as pg1

Note

For internal use only. Required for extending the class system of FindMyFriends.

thomasp85/FindMyFriends documentation built on April 25, 2020, 1:06 p.m.