Category (version 2.38.0)

makeChrBandGraph: Create a graph representing chromosome band annotation data

Description

This function returns a graph object representing the nested structure of chromosome bands (also known as cytogenetic bands). The nodes of the graph are band identifiers. Each node has a geneIds node attribute that lists the gene IDs that are annotated at the band (the gene IDs will be Entrez IDs in most cases).

Usage

makeChrBandGraph(chip, univ = NULL)

Arguments

chip

A string giving the annotation source. For example, "hgu133plus2"

univ

A vector of gene IDs (these should be Entrez IDs for most annotation sources). The annotations attached to the graph will be limited to those specified by univ. If univ is NULL (default), then the gene IDs are those found in the annotation data source.

Value

A graph-class instance. The graph will be a tree and the root node is labeled for the organism.

Details

This function parses the data stored in the MAP map from the appropriate annotation data package. Although cytogenetic bands are observed in all organisms, currently, only human and mouse band nomenclatures are supported.

Examples

chrGraph <- makeChrBandGraph("hgu95av2.db")
chrGraph