User: Robert Stojnic

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Posts by Robert Stojnic

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Comment: C: Motif enrichment analysis: Error in transfac format and background frequencies f
... Hi Dips, If you haven't already done so, please first update to the latest version of PWMEnrich (in release this is 3.6.1). I would recommend converting the MotifDb motifs directly into PFMs that PWMEnrich expects. The only issue here is that MotifDb motifs come from different sources and are not ...
written 5.1 years ago by Robert Stojnic80
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Answer: A: Motif enrichment analysis: Error in transfac format and background frequencies f
... Dear Deepti, If you want to use the mouse MotifDB motifs you can retrieve them in the correct format for PWMEnrich here: http://bioconductor.org/packages/2.14/data/experiment/html/PWMEnrich.M musculus.background.html Cheers, Robert On 07/09/14 16:47, deepti anand wrote: > Hi all, > I am s ...
written 5.1 years ago by Robert Stojnic80
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Comment: C: plotpfm has been removed in PWMEnrich?
... Dear Fabrice, This is because your PFM has very little information content. The only way to chop off the y axis (which might be misleading to your readers!) is to modify the plotting function. If you look at PWMEnrich:::seqLogoGrid() you will see these lines of code: if (ic.scale) { ylim ...
written 5.9 years ago by Robert Stojnic80
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Comment: C: plotpfm has been removed in PWMEnrich?
... Dear Fabrice, pm <- PFMtoPWM(pfm) plot(pm) will plot the logo with correct heights (it will use the calculation I've described below). More advanced options such as changing units (i.e. from bits to e.g. nats) are not supported. If you want to create a custom plot you will have to do it from s ...
written 5.9 years ago by Robert Stojnic80
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Comment: C: plotpfm has been removed in PWMEnrich?
... Hi Fabrice, The negative values are usual as the PWM matrix is defined as log2 probability_base / probability_background. So if the any of the probabilities is smaller than 0.25 in your input matrix, this will give a negative value. Maybe you wanted to get the heights of the individual letters in ...
written 5.9 years ago by Robert Stojnic80
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Answer: A: plotpfm has been removed in PWMEnrich?
... Dear Fabrice, You can plot the PFM in PWMEnrich by converting it to PWM: plot(PFMtoPWM(pfm_matrix)) Unfortunately the old function was deprecated. Sorry if it broke your code! Cheers, Robert On 07/12/13 04:41, Fabrice Tourre wrote: > Dear expert, > > I just want to plot PFM using PWME ...
written 5.9 years ago by Robert Stojnic80
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Rgraphviz and margins
... Hello, I am using Rgraphviz, first by calling layoutGraph() then renderGraph() on graphNEL. However, I cannot get the graph to be rendered with certain margins. I've tried the oldfashioned par(mar=...), tried passing the margin parameters to both layoutGraph and renderGraph, but nothing worked. Th ...
graph rgraphviz written 8.3 years ago by Robert Stojnic80 • updated 3.8 years ago by sebastian.wolf0

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