FindMyFriends (version 1.2.2)

collapseParalogues: Merge paralogue gene groups into new gene groups

Description

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

Usage

collapseParalogues(object, ...)
"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)