Pipeline for analyzing CNV (SNP array) level 3 from TCGA
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@ns-7498
Last seen 5.8 years ago
United States

I am wanna to make a matrix [sample x genes] from CNV files, level 3, downloaded from TCGA database, but I don't know how can I do that.

Currently I have mapped the segments to genes with help of guys, so I have many genes for each segment. It should be noted that some of segments have common genes and it have made me confused.

I appreciate if anyone can help and introduce texts.

EDIT: To be more clear, I have downloaded CNV (SNP array) for BRCA from TCGA. Its link is here.
SNP CNV TCGA • 3.5k views
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It would help to be more specific about the specific data that you have downloaded, e.g., referencing a particular file.

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You can find some of the files here.

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