constructAnnotationVectorSpace: For the argument 'genes' construct a vector space based on...

In asishallab/GeneFamilies: Analyses different properties of gene families

For the argument genes construct a vector space based on the distinct annotations found for the respective genes in arument annot.df. Each distinct annotation will be an axis, each gene will be assigned a vector, with coordinates the discrete number of times an annotation has been assigned to the respective gene.

Description

For the argument genes construct a vector space based on the distinct annotations found for the respective genes in arument annot.df. Each distinct annotation will be an axis, each gene will be assigned a vector, with coordinates the discrete number of times an annotation has been assigned to the respective gene.

Usage

constructAnnotationVectorSpace(genes, annot.df = all.ipr, gene.col = 1,
  annot.col = 2)

Arguments

genes	A character vector of gene IDs
annot.df	A data.frame or matrix holding the gene annotations. Default is all.ipr.
gene.col	The column name or number of annot.df in which to look up the gene IDs found in genes. Default is 1.
annot.col	The column name or number of annot.df in which to look up the genes annotations. Default is 2.

Value

NA if no annotations are found for any gene in genes, otherwise a data.frame with a column gene in which the gene IDs are held and one column for each distinct annotation or the respective vector space axes.

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