computeOrthologSpecificAnnotationDiversityPerGroup: Wrapper for function...

In asishallab/GeneFamilies: Analyses different properties of gene families

Wrapper for function computeSpeciesSpecificAnnotationDiversityPerGroup. Instead of species affiliation the distinction here is wether genes are Orthologs or Non-Orthologs.

Description

Wrapper for function computeSpeciesSpecificAnnotationDiversityPerGroup. Instead of species affiliation the distinction here is wether genes are Orthologs or Non-Orthologs.

Usage

computeOrthologSpecificAnnotationDiversityPerGroup(gene.groups.df,
  orthologs = orthologs.genes, group.col = "Family",
  gene.col = "Gene")

Arguments

gene.groups.df	An instance of base::data.frame with at least two columns. One must hold the gene group identifiers and the other the gene identifiers (accessions) belonging to the respective group.
group.col	The column name of 'gene.groups.df' in which to find the gene group identifiers. Default is 'Family'.
gene.col	The column name of 'gene.groups.df' in which to find the gene identifiers (accessions). Default is 'Gene'.

Value

An instance of base::data.frame with several columns. The first holds the gene group identifiers obtained from 'gene.groups.df' and one numeric column for each Orthologs and Non-Orthologs. The later columns hold the gene-class specific annotation entropies for the respective gene groups; NA values where no genes of that species were found to be members of the respective gene group.

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