selectGeneGroupSpecificEnrichedAnnotations: Infer enriched annotations specific to the argument type of...

In asishallab/GeneFamilies: Analyses different properties of gene families

Infer enriched annotations specific to the argument type of gene-groups, add human readable information to it and return it as a data.frame.

Description

Infer enriched annotations specific to the argument type of gene-groups, add human readable information to it and return it as a data.frame.

Usage

selectGeneGroupSpecificEnrichedAnnotations(gene.group.type,
  gene.group.type.enriched.annos = list(positively.selected =
  fams.pos.sel.non.conserved.iprs.enrich.df$Annotation, expanded.contracted
  = exp.fams.df.non.conserved.iprs.enrich.df$Annotation, tandems =
  bra8.tandem.clusters.non.conserved.iprs.enrich.df$Annotation, conserved =
  fams.conserved.non.conserved.iprs.enrich.df$Annotation),
  anno.db = ipr.db, anno.name = "NAME")

Arguments

gene.group.type	The type of the gene.groups for which to identify specific enrichments.
gene.group.type.enriched.annos	A list of enriched annotations per gene group. Names must include gene.group.type. Default is the enriched annotations found in this packages data.
anno.db	A list with names being the annotations as in the names of enriched.annotations and values are lists with a slot holding human readable information about the annotation.
anno.name	The slot name of the lists held in anno.db to extract for human readable information about the annotations.

Value

A data.frame with two columns: 1. Annotation and 2. Annotation.Name

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