count.rec.events.per.genome: Count number of overlapping recombination events at each...

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

Count number of overlapping recombination events at each genomic position

Description

This function reads a GFF file or data frame containing identified recombination events in the genome identified by Gubbins, and counts the frequency of recombination events at each genomic position i.e. number of unique overlapping recombination events. The data frame can be generated using the "load.gubbins.rec.events.gff" function

Usage

count.rec.events.per.genome(
  gubbins.gff.file,
  recom.input.type = "Gubbins",
  taxon.names
)

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.
taxon.names	Vector containing taxon names.

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

This function may take some minutes to finish depending on the number
of recombination events identifiedand genome size

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

rec.freq<-count.rec.events.per.base(gubbins.gff)

## End(Not run)

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