geneLocation: Get gene location for all genes

In FindMyFriends: Microbial Comparative Genomics in R

Description

This method returns the gene location of all genes as a data.frame with each row corresponding to a gene in the pangenome. The data.frame will have the columns 'start', 'end', 'contig' and 'strand' (order of columns not ensured) with start and end giving the start and end position of the gene on the contig/chromosome given in the contig column. Strand gives the direction of translation, 1 is from start to end and -1 is from end to start (thus start should always be lower than end no matter the direction of translation)

Usage

geneLocation(object)

## S4 method for signature 'pgInMemLoc'
geneLocation(object)

Arguments

object

A pgVirtual subclass

Value

A data.frame as described above

Methods (by class)

• pgInMemLoc: Get gene location for pgInMemLoc subclasses

Note

Required for subclasses of pgVirtualLoc in order to extend the class system of FindMyFriends

Examples

testPG <- .loadPgExample(geneLoc=TRUE)
head(geneLocation(testPG))

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