Question: Mean and median values in cn.mops cnvs output
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gravatar for kaushalm
5 months ago by
kaushalm0
kaushalm0 wrote:

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

 

cn.mops referencecn.mops • 253 views
ADD COMMENTlink modified 4 months ago by Bioconductor Community ♦♦ 0 • written 5 months ago by kaushalm0
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