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kaushalm
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@kaushalm-18939
Last seen 4.8 years ago
Hello,
I ran cn.mops in the tumor (2 samples per patient - primary and metastasis) and normal mode using function referencecn.mops. I am a little confused with the mean and median values in the output.
Here is an example:
| seqnames | start | end | width | strand | sampleName | median | mean | CN |
| chr20 | 1209048 | 1229463 | 20416 | * | 1410498_clean.bam | -1 | -0.9006 | CN1 |
| chr20 | 2673557 | 2686364 | 12808 | * | 1410498_clean.bam | 2.997577 | 2.6878 | CN1 |
| chr20 | 30156842 | 30195142 | 38301 | * | 1410498_clean.bam | -1 | -0.9962 | CN1 |
| chr20 | 31463687 | 31683019 | 219333 | * | 1410498_clean.bam | 0.584963 | 0.5372 | CN3 |
| chr20 | 58422134 | 58560184 | 138051 | * | 1410498_clean.bam | -1 | -0.9032 | CN1 |
The second row is a heterezygous deletion with integer copy number value of CN1. Why is the mean and median values for this segment greater than 0? For most of the other segments with loss the values are always < 0. Can someone kindly explain how this is calculated.
~Madhurima
