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

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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

1
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

dp

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

Value

An object of class Gene

Author(s)

Steffen Durinck and Jim Bullard

References

~put references to the literature/web site here ~

See Also

gdPlot

Examples

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##---- 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)
  }

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