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snystrom / memes

An R interface to the MEME Suite
https://snystrom.github.io/memes/
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rna option not recognised for runStreme #119

Closed CharlotteAnne closed 5 months ago

CharlotteAnne commented 5 months ago

Hi,

I am having an issue where the rna option isn't recognised by runStreme. My command is: memes::runStreme(down_prox_seq_200, ctrl_prox_seq_200, outdir = tempdir(), minw=3, maxw=5, rna=TRUE)

But in the output table the alphabet column is "DNA" and strand is "+-"

The version I am using is noted below:

packageVersion("memes")
[1] ‘1.10.0’

Alternatively, the rna=TRUE is recognised in runDREME.

Thanks for any help, Charlotte

snystrom commented 5 months ago

Hi Charlotte,

Could you try instead setting alph="rna"? This should do the same thing as the Boolean flag, and is in general the best way to hint the alphabet to use to any run function in {memes}. This is the one exception for how calling the functions in R slightly differs from the other command line arguments.

Hope this helps, let me know if it resolved your issue or not.

CharlotteAnne commented 5 months ago

Yes perfect!! Thanks so much!