User: bernatgel

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bernatgel100
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Posts by bernatgel

<prev • 20 results • page 1 of 2 • next >
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Comment: C: Replacement error in PermTest
... Great :) Glad it worked in the end. I've been bitten by this more than once! ...
written 8 days ago by bernatgel100
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Comment: C: Replacement error in PermTest
... Hi Alejandro, Can you check the size of the segments in "one"? I assume you are trying to represent segments of length 1, but BED is a 0-based format and you are representing segments of width 0. What's the output of `width(one)`? I think this might be at least part of the problem Bernat ...
written 9 days ago by bernatgel100
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Answer: A: Visualisation of ChIP-seq data in r - function errors in Gviz and biomaRt
... Hi @H. Chloe, I don't know why your code does not work, but since no one has given you an answer yet I'll suggest you an alternative to Gviz and Biomart. To plot this you can use [karyoploteR](http://bioconductor.org/packages/karyoploteR) instead of Gviz and the bioconductor annotation packages [Tx ...
written 10 days ago by bernatgel100
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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 11 weeks 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 11 weeks 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 12 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 5 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 15 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 16 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 16 months ago by bernatgel100

Latest awards to bernatgel

Scholar 2.2 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 3.4 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 3.6 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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