| GeneRegion-class {GenomeGraphs} | R Documentation |
Given a start and end position and a chromosome name, all gene structures in this region will be retrieved from Ensembl upon creation of the object.
Objects can be created by calls of the form new("GeneRegion", ...).
start:"numeric", start positionend:"numeric", end position chromosome:"character", chromosome name strand:"character", represents the strand from which the gene structures should be retrieved. Value is either + or -size:"numeric", represents the size of the GeneRegion in the final plot color:"character", represents the color to be used to plot the exons biomart:"Mart", containing the link to the Ensembl database. This should be created by the useMart function from the biomaRt packageens:"data.frame", output of the biomaRt query, should not be used by userssignature(.Object = "GeneRegion"): ... signature(.Object = "GeneRegion"): ... signature(object = "GeneRegion"): ... Steffen Durinck
http://www.stat.berkeley.edu/~steffen/
objects to See Also as gdPlot
if(interactive()){
mart = useMart("ensembl", dataset="hsapiens_gene_ensembl")
plusStrand = new("GeneRegion", chromosome = "17", start = 30450000, end = 30550000, strand = "+", biomart = mart)
genomeAxis = new("GenomeAxis", add53=TRUE)
gdPlot(list(genomeAxis, plusStrand), minBase = 30450000, maxBase = 30550000)
}