lncRNA from TCGA

Question

[jain72744]

Hi, how can I extract TCGA-LIHC data for long non-coding RNAs in R?

Answer 1

[Zhenyu Zhang]

Linc should be in the regular mRNA expression files. You just need to read the GTF for linc gene IDs.

[jain72744]

Okay, what is the difference between these IDs? And can they be extracted using code in R?

[ATpoint]

People here won't spoonfeed. Show some effort on what you tried. Take a GTF file that matches the TCGA annotations they used, subset for lncRNAs (it is annotated there) and then filter.