annotationEvolution: Measures annotations gained, lost, and shared between base...

In asishallab/GeneFamilies: Analyses different properties of gene families

Measures annotations gained, lost, and shared between base genes and evolved genes.

Description

Measures annotations gained, lost, and shared between base genes and evolved genes.

Usage

annotationEvolution(genes, gene.sets, base.gene.set = "ortholog",
  annot.df = all.ipr, gene.col = 1, annot.col = 2)

Arguments

genes	A group of genes in the form of a character vector of gene IDs
gene.sets	A named list defining base gene and evolved gene identifiers.
base.gene.set	The name of list-entry in gene.sets indicating which is to be interpreted as base genes. Default is 'ortholog'.
annot.df	A data.frame of gene annotations. Default is GeneFamilies::all.ipr
gene.col	The column name or index in annot.df in which to lookup the gene IDs. Default is 1
anno.col	The column name or index in annot.df in which to lookup the gene annotations. Default is 2.

Value

A data.frame with the following columns: n.gained, n.lost, n.shared, and total.

asishallab/GeneFamilies documentation built on May 22, 2023, 11:30 a.m.