makeGeneRegion {GenomeGraphs} | R Documentation |
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.
makeGeneRegion(start, end, chromosome, strand, biomart, dp = NULL)
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 |
An object of class Gene
Steffen Durinck and Jim Bullard
~put references to the literature/web site here ~
##---- 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) }