makeChrBandGraph {Category} | R Documentation |
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).
makeChrBandGraph(chip, univ = NULL)
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. |
This function parses the data stored in the
<chip>MAP
map from the appropriate annotation data package.
Although cytogenetic bands are observed in all organisms, currently,
only human band nomenclature is supported.
A graph-class
instance. The graph will be a
tree and the root node is labeled for the organism.
Seth Falcon
chrGraph <- makeChrBandGraph("hgu95av2") chrGraph