A coverageDataSet containing the coverage values for all genes.
method
A caracter vector indicating the method to be used.
outfile
A character vector indicating the output file name.
introns
An objet of type annotationsSet
containing the annotations of the intronic regions.
Note: The introns must have same name as the gene they
are associated with.
windowLength
If the method is "ratio", specify the length of the window to use
at each end of the gene.
iterations
If the method is "probabilistic", specify the number of iterations.