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Question: Analysing TCGA Level 3 Copy Number Data Location of markers in the genome
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gravatar for Luisa672
4 months ago by
Luisa6720
Luisa6720 wrote:

I have downloaded copy number alterations data from TCGA for Head and Neck cancer. I wanted to use the DNAcopy package and I need to create a CNA object (as described on the reference manual), however my data has both starts and ends which are different for each patient... I do not understand how to go from this to the locations (maploc) of the markers in the genome required to create said object. I have looked into some examples like the coriell data included with the package as well, but I can't seem to figure out how to get these values... Can someone please help me ? 

ADD COMMENTlink modified 4 months ago by markus.riester20 • written 4 months ago by Luisa6720
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gravatar for markus.riester
4 months ago by
markus.riester20 wrote:

A segmentation algorithm like CBS in DNAcopy takes normalized copy number data along the genome and identifies breakpoints where the copy number changes. So, if I understood correctly, the TCGA data you downloaded is already segmented and there is no need for DNAcopy. If you want to generate a matrix of copy number of all patients, have a look at the CNTools package. 

ADD COMMENTlink written 4 months ago by markus.riester20

Thank you very much for your answer!

What I initially wanted was to create a struct with the locations of the markers in the rows and the log values  in the columns (with each column corresponding to each patient). What I can't understand is how I get the locations, since for each patient I have two values (start and stop of the altered regions, different from patient to patient) and not just that one that seems to be the same across samples (however as I understand it I could assign a NaN if that region wasn't altered) ...

ADD REPLYlink written 4 months ago by Luisa6720

The level 3 TCGA data you downloaded does not provide this information. See https://cancergenome.nih.gov/abouttcga/aboutdata/datalevelstypes#11. The level 3 data is essentially the output what you would get by applying DNAcopy to level 2 data. 

ADD REPLYlink written 4 months ago by markus.riester20
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