How to creat a GRangesList object from TCGA CNV data

Question

[pyhgzzj]

How to creat a GRangesList object from TCGA CNV data? I need to calculate the CINdex of LIHC, one of the TCGA dataset, but I dont know how to create a GRangesList object from the TCGA CNV data. Thank you very much

[Ram]

1. What have you tried?
2. Why have you used the snp tag? It seems to be irrelevant to the question you're asking.

[ATpoint]

Most importantly, how do you data look right now?

[pyhgzzj]

I want to calculate the CINdex of TCGA LIHC

[pyhgzzj]

I want to calculate the CINdex of LIHC using TCGA data

Answer 1

[Kevin Blighe]

If you follow Part I, II, and III here, then you will have annotated recurrent somatic copy number alterations for your cancer of interest, as a GenomicRanges object: A: How to extract the list of genes from TCGA CNV data

Good luck

Kevin