How does TCGA get Segment_Mean in files of copy number variations?

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8.6 years ago

Ashleyca • 0

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.

RNA-Seq SNP genome sequencing • 2.3k views

ADD COMMENT • link 8.6 years ago by Ashleyca • 0

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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 REPLY • link 8.6 years ago by poisonAlien ★ 3.2k

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