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lima1 / PureCN

Copy number calling and variant classification using targeted short read sequencing
https://bioconductor.org/packages/devel/bioc/html/PureCN.html
Artistic License 2.0
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Annotation using different database #350

Open jennyp76 opened 8 months ago

jennyp76 commented 8 months ago

Hi, First of all, thank you for the wonderful tool. It been a lot of help.

I am trying to compare the total copy number between PureCN and CNVkit based on genes. So, comparing the total copy number of a gene detected from PureCN and CNVkit. Therefore, keeping the database used for annotation should be the same.

  1. Would there be a method to annotate genes using the 4th column of the BED file instead of TxDb.Hsapiens.UCSC.hg38.knownGene R package?
  2. And it this "https://hgdownload.soe.ucsc.edu/gbdb/hg38/knownGene.txt" is the annotation file used in PureCN for annotation?

Thanks, jen

Describe the issue A clear and concise description of what the issue is.

To Reproduce Copy and paste your complete command line arguments from PureCN.R. If possible and potentially relevant, also copy the output of NormalDB.R and Coverage.R.

Expected behavior A clear and concise description of what you expected to happen.

Log file Please copy and paste the log file (Sampleid.log) of a representative example

B-allele frequency plot Please take a screenshot of the B-allele frequency plot of the maximum likelihood solution (Sampleid.pdf).

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lima1 commented 8 months ago

That's a valid feature request. I'll see when I have time for this. If urgent, you probably for now are faster correcting the interval file gene column manually.