GP-class {AnnBuilder} | R Documentation |
This class is a sub-class of pubRepo with source specific functions to get/process data from GoldenPath {http://www.genome.ucsc.edu/goldenPath} to obtain gene location and orientation data
Objects can be created by calls of the form new("GP", ...)
.
A constructor (GP) is available and should be used to instantiate
objects of this class
organism
:"character", from
class "UG"
s character string for the organism of concernsrcUrl
:"character", from class
"UG"
a character string for the url where the source data
are. As multiple data sources will be used, srcUlr in this case is
the location where the source data are
(e.g. http://www.genome.ucsc.edu/goldenPath/14nov2002/database/)parser
:"character", from class
"UG"
not in usebaseFile
:"character", from
class "UG"
not in use
Class "UG"
, directly.
Class "pubRepo"
, by class "UG".
signature(object = "GP")
: Processes the
refLink and refGene data files and returns a matrix with gene
location and orientation dataThis class is part of the Bioconductor project at Dana-Farber Cancer Institute to provide Bioinformatics functionalities through R
Jianhua Zhang
# The example may take a few second to finish ## Not run: ## The url (\url{ftp://hgdownload.cse.ucsc.edu/goldenPath/currentGenomes/}) ## was correct at the time of coding. Replace with a correct one if it ## is invalid url <- getSrcUrl("GP", organism = "human") gp <- GP(srcUrl = url, organism = "human") strand <- getStrand(gp) ## End(Not run)