[Bioc-sig-seq] AlignedRead and complex subsetting

[Ivan Gregoretti]

Hello Everybody,

How do you subset an AlignedRead instance to keep (or reject) tags
that lay within a set of genomic regions?


Example

Lets say that I have an AlignedRead instance called aln.

Now let's say that I have a set of positions in BED style:

(chromosome, start end)
ch1 1000000 1000050
chrX 20000000 20100000
...(many more)...

We can imagine that I have the BED set loaded as a data frame.

Is it possible to pick from aln only the tags within (or outside) the
features defined in the table described above?

Thank you,

Ivan


Ivan Gregoretti, PhD
National Institute of Diabetes and Digestive and Kidney Diseases
National Institutes of Health
5 Memorial Dr, Building 5, Room 205.
Bethesda, MD 20892. USA.
Phone: 1-301-496-1592
Fax: 1-301-496-9878