makeGeneRegion: Creates an object of class Gene containing the intron-exon structures of genes

Description

Creates an object of class Gene containing the intron-exon structures of genes. Given a start and end position, strand and chromosome, all the intron-exon strcutures of all genes laying in this region will be retrieved.

Usage

makeGeneRegion(start, end, chromosome, strand, biomart, dp = NULL)

Arguments

start

Start position on chromosome

end

End position on chromosome

chromosome

Chromosome name

strand

Strand either + or -

biomart

Mart object, created by the useMart function of biomaRt

Object of class DisplayPars, determines the display of features on the plot

Value

An object of class Gene

References

~put references to the literature/web site here ~

Examples

Run this code

##---- Should be DIRECTLY executable !! ----
##-- ==>  Define data, use random,
##--	or do  help(data=index)  for the standard data sets.

## The function is currently defined as
function (start, end, chromosome, strand, biomart, dp = NULL) 
{
    if (missing(start)) 
        stop("Need to specify a start for creating a GeneRegion")
    pt <- getClass("GeneRegion")@prototype
    if (is.null(dp)) 
        dp <- pt@dp
    if (is.numeric(chromosome)) 
        chromosome = as.character(chromosome)
    new("GeneRegion", start = start, end = end, chromosome = chromosome, 
        strand = strand, biomart = biomart, dp = dp)
  }