Question: How does TCGA get Segment_Mean in files of copy number variations?
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gravatar for Ashleyca
2.6 years ago by
Ashleyca0
Ashleyca0 wrote:

Hi all,

I have download the copy number variation file of Ovarian serous cystadenocarcinoma in TCGA.

How does TCGA get Segment_Mean (please see the following image) in the of copy number variations files? Is there any algorithm to calculate the Segment_Mean? What is the algorithm?

enter image description here

The file shown in the above image was downloaded in: https://gdc-portal.nci.nih.gov/search/s

The following image show the position where the file was downloaded:

enter image description here

Thanks for any help.

sequencing snp rna-seq genome • 1.1k views
ADD COMMENTlink written 2.6 years ago by Ashleyca0

They are generated by circular binary segmenetation algorithm implemented in DNAcopy BC package. It basically looks for "change points" along the genome for amplifications and deletions.

ADD REPLYlink written 2.6 years ago by poisonAlien2.7k
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