TCGA CNV Files Segment Mean
How can we calculate copy number variation(gain/loss/amplification/deletion)based on segment mean value or segment median given in TCGA CNV file? Also suggest a reference to such calculation
• 13,196 views
•
link
updated
by
Ram
•
written
by
neenu.abraham8 •
•
written
by
neenu.abraham8 •
1 answer
I have given a full pipeline here, i.e., for taking the CN segment mean data and identifying recurrent gains and losses: C: How to extract the list of genes from TCGA CNV data
To then annotate the identified regions, take a look here: A: How to extract the list of genes from TCGA CNV data
Kevin
• 1 views
•
link
written
by
Kevin Blighe
Log in to answer this question.
More posts like this
-
How to get copy number gain/loss from TCGA gene_level_copy_number
written by NB •
-
How to interpret "pseudo count" in copy number data from CCLE?
written by lincaijin1994 •
-
How to check the frequency of CNV (amp or del) in TCGA CNV datasets ?
written by akshay_ware •
-
Can we estimate actual copy number using Segment_means in TCGA level 3 CNV data?
written by mbk0asis
-
What is the importance of probe no and segmentation mean in Copy Number Variation data
written by akij
-
Copy number analysis by Golden Helix
written by ytian •
-
Cancer Associated Frequent Copy Number Variations Regions (Gain)
written by Shicheng Guo
-
UCSC Xena CNV GISTIC2 (Threshold)
written by nijironohata •
-
genomic characteristics between copy number gain and loss
written by mangfu100
-
Copy number variation subtypes
written by neenu.abraham8 •
A similar question and some answers How To Process The Cnv Level 3 Data From Tcga
In general a zero value corresponding to CN2. You have to define a threshold for a deletion and duplication. This group used -0.2 and 0.2, respectively. http://mcr.aacrjournals.org/content/12/4/485.long
Thanks for your information....