accnet: Build accessory genome network (AccNET)

In irycisBioinfo/PATO: Pangenome Analysis Toolkit

Build accessory genome network (AccNET)

Description

Create an accnet object.

Usage

accnet(mmseqs, threshold = 0.8, singles = TRUE, dist = FALSE)

Arguments

mmseqs	An object od class mmseq
threshold	Remove proteins with a frequency higher than threshold (soft-coregenome).
singles	keep proteins presence in just one sample?
dist	pre calculate the distance matrix for further usage.

Details

This function extract the accessory genome from a mmseq object. The mmseq contains all the relationship among genomes (or other genomic unit) and genes/proteins. accnet extract the accsessory genome removing the sof-coregenome. Hard-coregenome is the set of proteins present in the 100\% of the genomes. Soft-coregenome is the set of proteins present in the threshold of the genomes.

Value

An accnet object.
accnet object contains

• list: Data.frame with the relationship of genome-protein

• matrix: Adjacency matrix (presence/absence)

• annot: Annotation table with the protein functional annotation

References

AcCNET (Accessory Genome Constellation Network): comparative genomics software for accessory genome analysis using bipartite networks VF Lanza, F Baquero, F de la Cruz, TM Coque - Bioinformatics, 2017

See Also

mmseqs

irycisBioinfo/PATO documentation built on Oct. 19, 2023, 3:07 p.m.