Recount3 uses the external ids

Question

Recount3 data correspond to TCGA data

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kevin lee • 0

@f4af91be

Last seen 21 months ago

China

I can't Correspond the data of recount3 with the TCGA data.I use the bcr patient uuid to do this thing, but I can't find the whole id.I want to ask if it has other methods？Thank you for your answer.

recount3 • 878 views

ADD COMMENT • link updated 6 hours ago by Leonardo Collado Torres ★ 1.1k • written 21 months ago by kevin lee • 0

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I want to add to this question, the recount3 repository uses other sampleIDs then TCGA. I know that before the IDs could be converted by using TCGAutils. However, GDC Legacy Archive has been retired and the archival data is no longer available. Causing the fact that UUIDtoBarcode(list_of_recount3_file_ids, from_type='file_id', legacy = T ) no longer works. I was wondering if there is another way to convert the recount3 sampleIDs to TCGA barcodes?

ADD REPLY • link 19 months ago seline.natalie • 0

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Hi,

This the solution to mapping TCGA ids in Recount3 to the ids used in the TCGA barcodes:

library(recount3)
human_projects <- available_projects()
#Example TCGA id
proj_info <- subset(
  human_projects,
  project == "ACC" & project_type == "data_sources"
)
rse_gene_ACC <- create_rse(proj_info)
rse_gene_ACC_expanded <- expand_sra_attributes(rse_gene_ACC)
rse_gene_ACC_metadata=data.frame(rse_gene_ACC_expanded@colData@listData)

Recount3 uses the external ids

> head(rse_gene_ACC_metadata$external_id)
[1] "43e715bf-28d9-4b5e-b762-8cd1b69a430e" "1a5db9fc-2abd-4e1b-b5ef-b1cf5e5f3872" "93b382e4-9c9a-43f5-bd3b-502cc260b886"
[4] "1f39dadd-3655-474e-ba4c-a5bd32c97a8b" "8c8c09b9-ec83-45ec-bc4c-0ba92de60acb" "85a86b91-4f24-4e77-ae2d-520f8e205efc"

TCGA barcode

> head(rse_gene_ACC_metadata$tcga.tcga_barcode)
[1] "TCGA-OR-A5KU-01A-11R-A29S-07" "TCGA-P6-A5OG-01A-22R-A29S-07" "TCGA-OR-A5K5-01A-11R-A29S-07" "TCGA-OR-A5K4-01A-11R-A29S-07"
[5] "TCGA-OR-A5LP-01A-11R-A29S-07" "TCGA-PK-A5H9-01A-11R-A29S-07"