User: bernatgel

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bernatgel100
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Posts by bernatgel

<prev • 17 results • page 1 of 2 • next >
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Answer: A: regioneR meanInRegions to evaluate mutation accumulation
... Hi Agnieska, I would recommend using mean in regions if you have precomputed levels of some magnitude per base or per genomic windows. An example of that could be the density of SNPs per megabase in a population level or the methylation values per CpG site determined by a Methylation array. On the ...
written 22 days ago by bernatgel100
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Answer: A: Is localZScore function of regioneR mask-aware?
... Hi Agnieszka, localZScore is not mask-aware. We've never needed until now, but it would be an interesting improvement of the function. We'll add the feature request to our TODO list and get back to you once it's implemented. Best, Bernat ...
written 27 days ago by bernatgel100
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Answer: A: Bioconductor - Karyoploter | Visualization | Multiple Chromosome display issue
... Hi Saeed, You can change the distance between chromosomes as well as the height of the ideogram or the data panels using the "plot.params" argument in `plotKaryotype`. In your case you'll probably want to increase the value of `data1outmargin` but there are many different parameters to adjust. You ...
written 4 weeks ago by bernatgel100
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Answer: A: regioneR ignore the strand information when using the extendRegions() function
... Hi @wuzefeng2008 The region management functions in regioneR does not take into account strand information at the moment. It's in our TODO list and strand management should be added by next Bioconductor release. Bernat ...
written 4 months ago by bernatgel100
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Comment: C: permutation test on one set of data to get p-value of highest peaks. permTest?
... I'm afraid regioneR will only tell you if all your regions at the same time, taken as a group, are closer to the boudaries than one would expect. It will not tell you which are the peaks that are closer.  There's plenty of documentation on how to create your own functions for example [here](https:/ ...
written 14 months ago by bernatgel100
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Comment: C: permutation test on one set of data to get p-value of highest peaks. permTest?
... @linuxborg2, you do not have a universe of all possible QKI peak position, so resample regions does not make sense. meanInRegions will compute the mean of a given value over the regions in A, but you do not have such a value. Please see my response below. ...
written 14 months ago by bernatgel100
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Answer: A: permutation test on one set of data to get p-value of highest peaks. permTest?
... Hi @linuxborg2, If I understand correctly your question, you want to know if QKI binding sites are positioned closer to to the intron-exon junctions than one would expect by chance. If this is correct, you can certainly use regioneR for that. In that case, you would need to give to `permTest`:   ...
written 14 months ago by bernatgel100
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Answer: A: RegioneR perm test result Plot- how is y axis calculated
... Hi Patrick, As you say, the x-axis of the perm tests plots depend on the evaluation function, in your case represents the number of overlaps between the two sets of regions. The y-axis, however, has always the same meaning: the probability density of the evaluation of the randomized region sets. Int ...
written 18 months ago by bernatgel100
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Answer: A: How to name the custom genome in karyoploteR ?
... Hi  @kirannbishwa01, It should work as you are doing but it for some reason it does not work with this BSgenome. karyoploteR ultimately relies on the function `getBSgenome` from `BSgenome` to load the necessary BSgenomes on the fly. As an example I tried downloading and installing `"BSgenome.Vvinif ...
written 18 months ago by bernatgel100
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Answer: A: Circos Tile colors
... I have successfully used Circos to plot copy number data, but I have no experience with OmicsCircos and similars. If you can accept a "linear" plot instead of circular you could take a look to karyoploteR. First create the sample data (with just two samples) and a few alterations. library(karyop ...
written 2.1 years ago by bernatgel100

Latest awards to bernatgel

Scholar 2.1 years ago, created an answer that has been accepted. For A: Retrieving Regions from hg38 of the same GC content and length with a list of el
Scholar 3.3 years ago, created an answer that has been accepted. For A: Retrieving Regions from hg38 of the same GC content and length with a list of el
Scholar 3.5 years ago, created an answer that has been accepted. For A: Retrieving Regions from hg38 of the same GC content and length with a list of el

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