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kkdey / Logolas

R package for Enrichment Depletion Logos (EDLogos) and String Logos
https://kkdey.github.io/Logolas-pages
GNU General Public License v3.0
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Convergence issue #19

Closed CDieterich closed 4 years ago

CDieterich commented 4 years ago

Great tool !

However, when I use: logomaker(A, type = "EDLogo", bg=apply(m6A,2,function(x){x/sum(x)}))

I get.. Analyzing the positional frequency matrix color_type not provided, so switching to per_row option for color_type frame width not provided, taken to be 1 frame width not provided, taken to be 1 Warnmeldung: In estimate_mixprop(data, g, prior, optmethod = optmethod, control = control, : Optimization failed to converge. Results may be unreliable. Try increasing maxiter and rerunning.

Is there a way to change/pass this parameter ?

kkdey commented 4 years ago

@CDieterich

The warning message comes from the ashr functionality that EDLogo uses for shrinkage. We have a recommend ash setting for EDLogo model and therefore, we did not offer the user control on tuning ash. However, this failure of convergence is not a big deal as the tolerance level of ash is very low, and EDLogo results usually change very little upon changing the maxiters and related controls on ash. I would suggest you can ignore this warning. Or you can use shrink=FALSE in logomaker if you so wish.

CDieterich commented 4 years ago

Thanks !