load.gubbins.GFF: Read recombination events from the output GFF file from...

In ChrispinChaguza/RCandy: RCandy: an R package for rapid visualisation of homologous recombination events in bacterial genomes

Read recombination events from the output GFF file from Gubbins

Description

This function reads a GFF format generated by Gubbins containing genomic regions where recombination events were identified.

Usage

load.gubbins.GFF(gubbins.gff.file, recom.input.type = "Gubbins")

Arguments

gubbins.gff.file	Path to the input Gubbins GFF recombination file or data frame
recom.input.type	Type of input recombination data, either "Gubbins" GFF or "BRATNextGen" tabular data.

Value

A data frame containing number of unique recombination events at genomic positions where recombination events were identified

Author(s)

Chrispin Chaguza, [e-mail]

References

https://github.com/ChrispinChaguza/RCandy

Examples

## Not run: 
Read genome in GFF formatted file (generated usign readseq) and plot the genomic features

gubbins.gff<-system.file("extdata", "ST320.recombination_predictions.gff", package = "RCandy",
mustWork = TRUE)

rec.events<-load.gubbins.rec.events.gff(gubbins.gff)

## End(Not run)

ChrispinChaguza/RCandy documentation built on June 23, 2022, 1:03 p.m.