[Bioc-sig-seq] Feature request: matchPWM() and DNA reverse complement.

[Ivan Gregoretti]

Hi everybody,

Wouldn't it be great if matchPWM() optionally searched for matches on
the reverse complement of its subject?


Currently, we can do this by running

A <- matchPWM(pwm, subject)
B <- matchPWM(reverseComplement(pwm), subject)

followed by merging A and B and finally sorting by coordinate.

The actual production code looks quite awkward but I want to keep it simple.

It would be light-speed fast if you could just

matchPWM(pwm,subject,also.reverse=TRUE)

Granted that the output should also display a strand column but I hope
users would not find this feature too inconvenient.

Please hold this request into consideration

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: 1-301-496-1016 and 1-301-496-1592
Fax: 1-301-496-9878