collapseParalogues: Merge paralogue gene groups into new gene groups

In thomasp85/FindMyFriends: Microbial Comparative Genomics in R

Description

This method allows for merging of paralogue gene groups defined using kmerLink into new, bigger, gene groups.

Usage

collapseParalogues(object, ...)

## S4 method for signature 'pgVirtual'
collapseParalogues(object, combineInfo = "merge",
  ...)

Arguments

object	A pgVirtual subclass
...	parameters passed on to metadata collapse function. For combineInfo='merge' sep specifies the separator - sep='none' collapses information into list elements instead of strings. For combineInfo='largest' no addition arguments are given.
combineInfo	The approach used to combine metadata from the collapsed groups. Either 'merge' for merging, 'largest' for picking information from the largest group, or a function that takes a data.frame of multiple rows and converts it to a data.frame with one row and the same columns.

Value

An object of the same class as object with the new grouping.

Methods (by class)

• pgVirtual: Merge paralogue gene groups for all pgVirtual subclasses

Examples

testPG <- .loadPgExample(withGroups=TRUE, withParalogues=TRUE)

# Number of gene groups before collapse
nGeneGroups(testPG)

# Number of gene groups after collapse
testPG <- collapseParalogues(testPG, combineInfo='largest')
nGeneGroups(testPG)

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