User: bernatgel

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bernatgel120
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Spain
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4 years, 11 months ago
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Posts by bernatgel

<prev • 24 results • page 1 of 3 • next >
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Answer: A: behaviour of regioneR permTest function
... Hi @shoko I think the numbers you are seeing are the expected result (mostly). Randomize regions will randomly place the regions into the available genome, **possibly overlapping** (see ?randomizeRegions). This means that the 3 regions might end up in chr2, and in fact this is what happens most of ...
written 11 weeks ago by bernatgel120
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Comment: C: How to add a color legend to plotKaryotype and kpPlotRegions ?
... Hi again, I just found out you can use `karyoploteR` with `grid`, `cowplot` and `patchwork` using the package `ggplotify`. You can find the code in this [github issue](https://github.com/bernatgel/karyoploteR/issues/51). ![enter image description here][1] [1]: https://raw.githubusercontent.co ...
written 3 months ago by bernatgel120
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Comment: C: How to add a color legend to plotKaryotype and kpPlotRegions ?
... Hehe! glad you find it useful! karyoploteR is pure base graphics and so it's not possible to store it in a variable to plot later. Actually, karyoploteR plays really bad with graphics composition packages such as grid or the base `par(mfrow=(A,B))`. This is something I'd like to improve in the futu ...
written 3 months ago by bernatgel120
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Answer: A: How to add a color legend to plotKaryotype and kpPlotRegions ?
... Hi Aditya, You can use legend as you would use with any other plot. kp <- karyoploteR::plotKaryotype('mm10') granges1 <- GenomicRanges::GRanges(c('chr1', 'chr2'), c('100-200', '100-200')) granges2 <- GenomicRanges::GRanges(c('chr3', 'chr4'), c('100-200', '100-200')) karyop ...
written 3 months ago by bernatgel120
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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 5 months ago by bernatgel120
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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 5 months ago by bernatgel120
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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 5 months ago by bernatgel120
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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 7 months ago by bernatgel120
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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 7 months ago by bernatgel120
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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 7 months ago by bernatgel120

Latest awards to bernatgel

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
Scholar 3.8 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 4.1 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

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