collectNonConservedAnnotations: For each species identifies those annotations that are non...

In asishallab/GeneFamilies: Analyses different properties of gene families

For each species identifies those annotations that are non conserved within those gene groups (e.g. families) that are indicated by group.ids. Non conservation is inferred by nonConservedCompositeAnnotations(...).

Description

For each species identifies those annotations that are non conserved within those gene groups (e.g. families) that are indicated by group.ids. Non conservation is inferred by nonConservedCompositeAnnotations(...).

Usage

collectNonConservedAnnotations(genes.df, group.col = "Tandem.Cluster",
  group.ids = unique(genes.df[, group.col]), gene.annos = all.ipr,
  annos.gene.col = 1, annos.anno.col = 2)

Arguments

genes.df	A data.frame with three columns, two of which need to be named 'Gene' and 'Species'. The first column needs to hold the gene-group IDs.
group.col	Identifies the column of genes.df in which to lookup gene-group-identifiers. Default is 'Tandem.Cluster'.
group.ids	Vector holding indicating in which gene-groups to look for non conserved composite annotations. Default is unique(genes.df[, group.col]).
gene.annos	The data.frame holding the annotations for the genes in 'gene.accs'. Default is all available InterPro annotations expected to be found in 'all.ipr'
annos.gene.col	The column of gene.annos in which to lookup the gene identifiers or gene accessions. Default is 1
species	The species for which to identify non conserved composite annotations. Default is unique(genes.df$Species).
anno.col	the column of gene.annos in which to lookup the function annotation for the genes in 'gene.accs'. Default is 2

Value

A data.frame with four columns: 1. The names of the gene-groups, 2. Species, 3. genes, and 4. the non conserved annotations (now non-composite!).

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