Where to get the molecular subtype information of STAD sample in TCGA

Question

[younglin113]

I want to obtain the molecular subtype information of STAD samples from TCGA, but I downloaded the clinical file from GDC and the phenotype file from UCSC xena, neither of them includes the subtype information. Does anyone happen to have idea where to get this information? Many thanks.

[Hamid Ghaedi]

Give TCGAbiolinks package a try.

[younglin113]

Thanks a lot! But still a bit curious why this information is not included in GDC or UCSC xena.

[Zhenyu Zhang]

You are talking about publication level data analysis that has manual steps involved. GDC might add function to allow molecular clustering, but won't include information from a particular paper about a particular subset of samples if the method is not uniformly accepted. Overall, this is not clinical data at all.