pangenomes_from_mmseqs: Creates Pangenomes from mmseqs object

In irycisBioinfo/PATO: Pangenome Analysis Toolkit

Creates Pangenomes from mmseqs object

Description

Creates clusters of genomes (pan-genome) using a list of pre-defined clusters. The list of cluster can be from external source (e.g. mlst or BAPS) or from an internal function (e.g clustering function). Moreover, pan-genomes can be filtered by genome frequency (i.e. the number of genomes that belong to the pangenome). pangenomes builds a new accnet object that relates the pangenome with the genes/proteins. The user can filter the proteins that are included by the presence frequency.

Usage

pangenomes_from_mmseqs(
  data,
  cluster,
  min_freq = 0,
  max_freq = 1,
  min_pangenome_size = 1
)

Arguments

data	A mmseq object
cluster	A data.frame with two columns: strain label (ID) and cluster. Colnames are not required. Cluster column can be any categorical variable.
min_freq	Minimun gene/protein frequency to include in the pangenomes.
max_freq	Maximun gene/protein frequency to include in the pangenomes.
min_pangenome_size	Minimun number of genomes to create a new pangenome.

Value

An accnet object.

See Also

clustering

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