User: bernatgel
bernatgel • 1.8k
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Posts by bernatgel
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... You can use [karyoploteR](http://bioconductor.org/packages/release/bioc/html/karyoploteR.html) as Bastien suggested, but if you can a whole genome coverage plot I think the best approach would be to perform a bit of preprocessing instead of going directly to `kpPlotCoverage`.
I would recommend usi ...
written 10 days ago by
bernatgel • 1.8k
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... It should run without any problem... it's been available for the last few Bioconductor releases.
Did you try with BiocManager::install("karyoploteR")? Since it's a Bioconductor package it cannot be installed with `install.packages()` but with `BiocInstaller::install()`. You have the exact code at th ...
written 12 days ago by
bernatgel • 1.8k
2
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2
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... If you want to plot them, you can use [karyoploteR](http://bioconductor.org/packages/karyoploteR/). The function [kpPlotRegions](https://bernatgel.github.io/karyoploter_tutorial//Tutorial/PlotRegions/PlotRegions.html) plot the regions non-overlapping by default and will create the plot I think you a ...
written 13 days ago by
bernatgel • 1.8k
1
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1
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362
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1
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Comment:
C: How to do survival analysis?
... I agree with the answer but I would just add that you need to take into account multiple testing! If you are testing all genes to see if they correlate with survival you are doing 20k hypothesis tests. You need the probability of finding something "statistically significant" just by chance without a ...
written 15 days ago by
bernatgel • 1.8k
0
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162
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... If you have R installed, it should be fairly easy to install.
if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager")
BiocManager::install("karyoploteR", version = "3.8")
If you need more than this, feel free to ask.
BTW, to run this exact code you will need ...
written 28 days ago by
bernatgel • 1.8k
6
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2
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162
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... I don't know the exact software used to create that image but you can reproduce it using [karyoploteR]( http://bioconductor.org/packages/karyoploteR/).
![reproduction of the DMR plot using karyoploteR][1]
Here's the code. We start creating random regions on the genome with [regioneR](http://biocon ...
written 4 weeks ago by
bernatgel • 1.8k
1
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3
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3.6k
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3
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... The function `toGRanges` from package [regioneR](http://bioconductor.org/packages/regioneR/) will work both with a data frame or a file with a bed-like structure (it will internally call rtracklayer::import used by igor to actually import the data)
library(regioneR)
dd <- toGRanges("d ...
written 4 weeks ago by
bernatgel • 1.8k
1
vote
3
answers
171
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3
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... Sure, to have all chromosomes in one line use
kp <- plotKaryotype(plot.type=4)
and keep everything else the same. There are various plot types available to choose from. You can find them in [the tutorial page](https://bernatgel.github.io/karyoploter_tutorial//Tutorial/PlotTypes/PlotTypes.ht ...
written 5 weeks ago by
bernatgel • 1.8k
2
votes
3
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171
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3
answers
... Hi sm.hasehmin,
You can use the Bioconductor package [karyoploteR](http://bioconductor.org/packages/karyoploteR/) for this. You can plot the data as points using [kpPoints](https://bernatgel.github.io/karyoploter_tutorial//Tutorial/Points/Points.html) as in the example below or you could change tha ...
written 5 weeks ago by
bernatgel • 1.8k
3
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3
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187
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3
answers
... If you want to know what genes are affected by the variants in the VCF file what you should do is **annotate** the VCF. There are many tools for that and wouldn't recommend doing that with your own code.
For example
- [Annovar](http://annovar.openbioinformatics.org/en/latest/)
- [VEP](https://www. ...
written 7 weeks ago by
bernatgel • 1.8k
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