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Visualizing called somatic copy number variation
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12 months ago
F ♦ 3.4k
Iran

Hi,

I have called somatic copy number variation from WGS for tumor and its matched model (of course related to matched normal) by scatngs

scatngs gave me 3 filee for each sample and its matched normal, one of them is this table

> head(copynumber[1:4,])
            X Chromosome Position      Log.R segmented.LogR    BAF segmented.BAF Copy.number Minor.allele
1  rs62635286          1    13116 -1.2304076    0.001603515 0.0000     0.3176833           2            1
2  rs75454623          1    14930 -0.3908885    0.001603515 0.3548     0.3176833           2            1
3    rs806731          1    30923         NA    0.001603515     NA            NA           2            1
4 rs200943160          1    49298 -0.6588803    0.001603515 0.0000            NA           2            1
  Raw.copy.number
1       0.4136176
2       1.1914908
3              NA
4       0.8499854
>

I am seeing people plot something like this in their papers

enter image description here

I need an intuition please how to get such plot with my data. Thanks for any suggestion

WGS CNV • 180 views
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I am seeing people plot something like this in their papers

Sounds like it could be a popular package, then. I'd use ggplot2::geom_rect with various aesthetics linked to various dataset attributes, but a package might make life easier for you. If you could give a few sample papers, we should be able to find the package being used.

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Thank you, people usually say how they called the copy number but not mentioning how they plot like this for example in this paper https://www.ncbi.nlm.nih.gov/pubmed/29853643 , figure 1D

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It might help to email the authors. There is not much information about the tool used in the paper. Are there other papers that have a similar graph? If not, the authors might have just used custom ggplot.

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