seqToGeneGroup: Get gene-to-genegroup relationship

In FindMyFriends: Microbial Comparative Genomics in R

Description

This method returns the group membership for each gene in the pangenome as a vector of indices. Element 1 corresponds to gene 1 and the value is the index of the corresponding gene group. If gene groups have yet to be defined it returns a vector of length 0.

Usage

seqToGeneGroup(object)

## S4 method for signature 'pgInMem'
seqToGeneGroup(object)

Arguments

object

A pgVirtual subclass

Value

An integer vector with an element for each gene in the pangenome.

Methods (by class)

• pgInMem: Gene to genegroup indexing for pgInMem subclasses

Note

Required for extending the class system of FindMyFriends

See Also

seqToOrg for gene-to-organism relationship

Examples

testPG <- .loadPgExample(withGroups=TRUE)

# Have a look at what the first six genes belongs to
head(seqToGeneGroup(testPG))

FindMyFriends documentation built on Nov. 8, 2020, 6:46 p.m.