Hi Matt
It looks like you are trying to obtain the upstream sequence data
information given transcription factor binding sites???
There are a lot of functions in Bioconductor which are optimized for
this type of analysis. If you wish to either post on the Bioconductor
mailing list (https://support.bioconductor.org/), or tell me a little
more, I can perhaps help.
Also see
http://bioconductor.org/help/search/index.html?q=transcription+factor+binding/.
There are several workflows and lots of docs on TFBS analysis.
Also Matt as you are local to Boston, I am happy to point you to local
Boston resources if you are new to R/Bioconductor.
Best
Aedin
--
Aedin Culhane
---------------
Department of Biostatistics and Computational Biology,Dana-Farber Cancer
Institute
Department of Biostatistics, Harvard TH Chan School of Public Health
email: ae...@jimmy.harvard.edu
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