ChrBandTree-class {Category} | R Documentation |
This class represents chromosome band annotation data for a given experiment. The class is responsible for storing the mapping of band to set of gene IDs located within that band as well as for representing the tree structured relationship among the bands.
Objects should be created using NewChrBandTree
or
ChrBandTreeFromGraph
.
toParentGraph
:"graph"
representing the tree of chromosome bands. Edges in this directed
graph go from child to parent.toChildGraph
:"graph"
. This is
the same as toParentGraph
, but with the edge directons
reversed. This is not an ideal implementation due to the
duplication of data, but it provides quick access to parents or
children of a given node.root
:"character"
giving the
name of the root node. The convention is to use "ORGANISM:<organism>".level2nodes
:"list"
providing a
mapping of levels in the tree to the set of nodes at that level.
Levels X
is defined as the set of nodes with a path length of
X
from the root node.ChrBandTree
n
. Each element is a character vector of
node names of the children of the named element.childrenOf
for a description of the structure of the return
value.level
. The level
argument can
be either numeric or character, but should match a level returned by
treeLevels
.Not all known chromosome bands will be represented in a given instance. The set of bands that will be present is determined by the available annotation data and the specified gene universe. The annotation source maps genes to their most specific band. Such bands and all bands on the path to the root will be represented in the resulting tree.
Currently there is only support for human and mouse data.
S. Falcon
library("hgu95av2.db") set.seed(0xfeee) univ = NULL ## use all Entrez Gene IDs on the chip (not recommended) ct = NewChrBandTree("hgu95av2.db", univ) length(allGeneIds(ct)) exampleLevels(ct) geneIds(ct, "10p11") lgeneIds(ct, "10p11") lgeneIds(ct, c("10p11", "Yq11.22")) pp = parentOf(ct, c("10p11", "Yq11.22")) childrenOf(ct, unlist(pp)) treeLevels(ct) level2nodes(ct, 0) level2nodes(ct, 0L) level2nodes(ct, "0") level2nodes(ct, 1)