nonConservedAnnotations: Identifies those gene annotations that are non conserved...

In asishallab/GeneFamilies: Analyses different properties of gene families

Identifies those gene annotations that are non conserved within the argument gene-group. Non conserved is inferred as those annotations that do not appear or miss from the most frequent composite annotation.

Description

Identifies those gene annotations that are non conserved within the argument gene-group. Non conserved is inferred as those annotations that do not appear or miss from the most frequent composite annotation.

Usage

nonConservedAnnotations(gene.accs, gene.annos = all.ipr, gene.col = 1,
  anno.col = 2, rm.genes.without.annos = TRUE)

Arguments

gene.accs	Character-Vector of gene-IDs.
gene.annos	A data.frame of gene annotations
gene.col	The column of gene.annos in which to lookup the gene IDs. Default is 1
anno.col	The column of gene.annos in which to lookup the gene annotations. Default is 2
rm.genes.without.annos	If set to TRUE genes without any annotation are ignored, otherwise this will cause all conserved annotations to appear in the result. Default is TRUE

Value

A data.frame with two columns: 'Gene' holds the gene identifiers of genes that have non conserved annotations, and column 'Non.Conserved.Annotation' holds the respective annotations.

asishallab/GeneFamilies documentation built on July 28, 2024, 11:44 a.m.