User: bernatgel

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bernatgel90
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Posts by bernatgel

<prev • 13 results • page 1 of 2 • next >
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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 3 months ago by bernatgel90
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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 3 months ago by bernatgel90
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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 3 months ago by bernatgel90
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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 8 months ago by bernatgel90
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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 8 months ago by bernatgel90
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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 14 months ago by bernatgel90
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Comment: C: Error running the function permTest
... Hmm... I think it might come from an unavailable genome, although the error message should be quite more clear.  Could you check if the genome is available with  installed.genomes() You should see "BSgenome.Hsapiens.UCSC.hg19.masked" in the output. If it's not installed, try installing it with ...
written 15 months ago by bernatgel90
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Answer: A: Error running the function permTest
... I just run the full example in and it run without errors for me.  If you take a closer look at the error message it produced you can see it said 1: In mclapply(c(1:ntimes), randomize_and_evaluate, ...) : all scheduled cores encountered errors in user code That means that all parallel jobs sent e ...
written 15 months ago by bernatgel90
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Answer: A: how to plot human genome chromosome Ideogram with each length by Gviz
... You can use karyoploteR for that. You can create the complete ideograms for many different genomes (even for custom ones) and plot data on it if you want. IMPORTANT: karyoploteR is only available in Bioconductor devel until next release (mid April 2017) To create a simple ideogram of the human gen ...
written 16 months ago by bernatgel90
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Answer: A: Conflicting results in 'overlapPermTest' function from regioneR package
... Hi Vinicius, The problem may be due to how the overlaps are counted. When a region in A overlaps multiple regions in B it can be counted as one or multiple overlaps. By default, the function numOverlaps in regioneR counts them as multiple overlaps while your code counts the overlap only once. Actua ...
written 18 months ago by bernatgel90

Latest awards to bernatgel

Scholar 14 months 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 2.4 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 2.6 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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