memes
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snystrom
An R interface to the MEME Suite
This might have to do with inheritance of previous named state of this column. But check when running from .meme path also. Could require an additional modification to the import...
- [ ] Loaded/excluded database entries (print to terminal) test: - [ ] more than 1 db produces correct output (need to left_join on db + idx cols, or is...
setting `outdir` will overwrite. Unclear if it overwrites target files, or the whole dir. If it's the whole dir, this option needs to be removed or you could accidentally `outdir...
Fasta files need headers, so check that there are names in the biostring object. - [ ] write unit tests checking runDreme/runAme/ etc. with sequences lacking names
anywhere I set `e = 50` is bad because it gives the wrong impression for how it should be used. Other ways to get fast running example that returns data??
This should be kept consistent. Or at least, I need some feedback on how to deal with this. What I don't like is when people show plots of the PWM...
Allow value1, value2 to be configurable, each generates a CDF based on that data parameter. Value2 default = "normalize"
DREME replacement (keep runDreme). Faster, better, bigger motifs. Authors now suggest STREME for >=50 sequences, MEME for
New tool for testing enrichment of known motif relative to another set (or shuffle). This seems very useful. It uses same objective function as STREME. http://meme-suite.org/doc/enr.html "The program uses Fisher's...
This would be a nice little convenience function. Q: also need to reexport generic?? Like so: ```{r} view_motifs.data.frame