How does TCGA get Segment_Mean in files of copy number variations?
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?
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:
Thanks for any help.
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Ashleyca •
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How does TCGA get Segment_Mean in files of copy number variations?
written by Ashleyca •
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.