plot.gene.peaks: Creates a pile up of bed files using the Sushi R package
In helen-zhu/DPDE4PM: A Method for Peak Merging Across Biological Replicates

Creates a pile up of bed files using the Sushi R package

## S3 method for class 'gene.peaks'
plot(
  GENE,
  PEAKS,
  GTF = NULL,
  ANNOTATION = NULL,
  OUTPUTDIR = ".",
  OUTPUT.TAG = "",
  PLOT = T
)

`GENE`	A 'character' gene id corresponding to the gene_id's found in the GTF files and the 'name' column in the peak files
`PEAKS`	data frame containing the following columns, and potentially extras, usually found in a BED12 file, base 0 system chr chromosomes, same as in GTF file start starting position of the peak, base 0 end end position of the peak, base 0 name gene id score p-value associated with the peak strand strand of the gene blockCount number of segments in the peak blockSizes size of segments in the peak, BED12 notation blockStarts starting positions of segments, BED12 notation sample sample_id of samples
`GTF`	The GTF file used to generate the peaks. This is used to determine the genomic coordinates of the gene.
`OUTPUTDIR`	Output directory
`OUTPUT.TAG`	A character string indicating a tag to track the generated files
`PLOT`	Binary T or F indicating whether to save plot or just return plot