PSCBS segmentation file header
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5.6 years ago
vakul.mohanty ▴ 260

Hello,

I'm have used Paired parent specific circular binary segmentation (PSCBS) to segment copy number calls made from SNP6 data and obtain copy numbers as well as LOH calls. I'm however having trouble interpreting some of the columns in the segmentation file. (tcnNbrOfLoci, tcnNbrOfSNPs, tcnNbrOfHets, dhNbrOfLoci). I'm unable to find the documentation that clarifies what these columns mean. I'll be grateful for any information on these columns or directions to the appropriate documentation.

I have also attached an snippet of the actual segmentation file for clarification.

Thanking You, Vakul

chromosome  tcnId   dhId    start   end tcnNbrOfLoci    tcnMean tcnNbrOfSNPs    tcnNbrOfHets    dhNbrOfLoci dhMean  c1Mean  c2Mean  rohCall abCall  lohCall ntcnCall

1   1   1   61736   356493.5    29  2.0454  0   0   0   NA  NA  NA  NA  NA  NA  TRUE

1   2   1   356493.5    41027889.5  22688   1.5614  3209    3209    3209    0.0956  0.70606508  0.85533492  FALSE   FALSE   FALSE   TRUE

1   3   1   41027889.5  41666838.5  354 1.7366  45  45  45  0.111   0.7719187   0.9646813   FALSE   FALSE   FALSE   TRUE
CNV parent spcific copy number aroma SNP6 • 1.4k views
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Please format your question and data properly

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5.6 years ago
Eric T. ★ 2.7k

The reference manual and two example code vignettes are on the CRAN page for PSCBS: https://cran.r-project.org/web/packages/PSCBS/index.html

The peer-reviewed paper is quite readable and explains the core concepts well, e.g. total copy number (TCN), runs of homozygosity (ROH), and how they're calculated. https://academic.oup.com/bioinformatics/article/27/15/2038/401729/Parent-specific-copy-number-in-paired-tumor-normal

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