Definition of some of the columns in PSCBS segmentation file
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@vakulmohanty-8232
Last seen 4.4 years ago
United States

Hello,

I used PSCBS and the aroma package to obtain copy number from tumor normal pairs. The code runs fine and I end up with a text file with copy number of segments. I'm however unable to figure out the meaning of some of the columns in the result file(tcnNbrOfLoci, tcnNbrOfSNPs, tcnNbrOfHets, dhNbrOfLoci). I'm also unable to find documentation that clarifies what these columns are. I'll be grateful for any explanation on what these columns stand for or a pointer to the appropriate documentation.

I have also attached a snippet of the result file below.

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

aroma.light affiymetrix SNP6 PSCBS parent specific copy number • 460 views
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