Error in optim(init, fn = loglik_per_TF, gr = deriv_per_TF, lower = 10^(-16), : L-BFGS-B needs finite values of 'fn' (not related to GC content)

[nevelsk90]

Hi,

Thanks for making the tool,

Unfortunately I get the same error even when GC content is not equal zero.
Please download R object with input files using the link : https://drive.google.com/open?id=19HZIcR5CGBwDod-Ht0jSnHBsYynGPhJB

I should say that the file containing instances of motifs (GRmotif) is NOT a result of footprint calling but of motif scanning with FIMO. But if I understand correctly BiFET should be able to process these results as well.

Thank you in advance and regards
TIm

Originally posted by @nevelsk90 in #1 (comment)

[nlawlor]

Hi Tim,

Thanks for your interest in BiFET! I took a look at your R object and both GRpeaks/GRmotif objects seem properly formatted. Yes, I believe BiFET should be able to handle footprint calls from other methods, including FIMO.

I'm not sure what may be the issue here with the optimization function but @youna2 and I will take a deeper look into this and hopefully get back to you soon!

Thanks,
Nathan