Question

How to creat a GRangesList object from TCGA CNV data

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5.7 years ago

pyhgzzj • 0

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

SNP • 1.1k views

ADD COMMENT • link updated 5.7 years ago by Kevin Blighe 90k • written 5.7 years ago by pyhgzzj • 0

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

ADD REPLY • link 5.7 years ago by Ram 45k

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Most importantly, how do you data look right now?

ADD REPLY • link 5.7 years ago by ATpoint 90k

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I want to calculate the CINdex of TCGA LIHC

ADD REPLY • link 5.7 years ago by pyhgzzj • 0

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I want to calculate the CINdex of LIHC using TCGA data

ADD REPLY • link 5.7 years ago by pyhgzzj • 0

score 0 · Answer 1 · 2020-03-01

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5.7 years ago

Kevin Blighe 90k

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

ADD COMMENT • link 5.7 years ago by Kevin Blighe 90k