ICI data tagged as TCGA

[Gibbsdavidl]

library(iatlasGraphQLClient) dataset_tags <- iatlasGraphQLClient::query_dataset_tags() dataset_tags[dataset_tags$tag_name == 'TCGA_Study',]

Table returned includes: "TCGA_Study" "TCGA Study" "TCGA Study" NA NA "Chen 2016 - SKCM, Anti-CTLA4" "Chen_CanDisc_2016" "TCGA_Study" "TCGA Study" "TCGA Study" NA NA "Choueiri 2016 - KIRC, PD-1" "Choueiri_CCR_2016" "TCGA_Study" "TCGA Study" "TCGA Study" NA NA "Gide 2019 - SKCM, PD-1 +/- CTLA4" "Gide_Cell_2019"

In the 6th column, those are ICI data sets, not part of TCGA.

[heimannch]

This query returns which datasets have annotation for TCGA_Study. What I understand you want to get can be achieved with:

tcga_studies <- iatlasGraphQLClient::query_tags_with_parent_tags(parent_tags = "TCGA_Study")
tcga_studies$tag_name

[Gibbsdavidl]

Oh, my issue was that ICI data sets were tagged with "TCGA_Study" as above.
For example, the "Choueiri 2016 - KIRC, PD-1" data is not from TCGA, yeah?

[andrewelamb]

I think that means that those ICI patients have been labeled using the 33 "TCGA_Study" cancer types.

[Gibbsdavidl]

OK, thanks!