intersect_cgi_tss: Keep CGIs that intersect with promoter regions
In andreaskapou/processHTS: Process HTS Files and Data

intersect_cgi_tss keeps only CpG islands that overlap with promoter regions N bp upstream and M bp downstream of TSS.

1
2
3

intersect_cgi_tss(cgi_file, rna_files, chrom_size_file = NULL,
  chr_discarded = NULL, upstream = -100, downstream = 100,
  unique_tss = FALSE)

`cgi_file`	The name of the CGI '.bed' formatted file to read data values from.
`rna_files`	The name of the RNA-Seq '.bed' formatted file to read data values from.
`chrom_size_file`	Optional name of the file containing genome chromosome sizes
`chr_discarded`	A vector with chromosome names to be discarded.
`upstream`	Integer defining the length of bp upstream of TSS.
`downstream`	Integer defining the length of bp downstream of TSS.
`unique_tss`	Logical, indicating if CGIs should match only to unique TSS, default false, so as to consider strand direction.