extract from ID case the ID files

[bioinfo-dirty-jobs]

I want create a manifest file where I have my UIDD from case and UIDD from Files.

uuids = c("34C39A6B-DB6A-47E5-B0D4-5FA990EF7EB8",
"AAF93A92-2F93-477D-9EA4-D18AB7D4F258",
"F6509C51-3BDC-45CC-81FE-5E775236305A",
"F94615EA-551C-4F63-AF0D-5E49C87FC66E")

data3=files() %>% 
    filter( ~ cases.case_id %in% tolower(uuids) &
                        data_type == "Gene Expression Quantification" &
                        analysis.workflow_type=="HTSeq - Counts") %>% 
    manifest()
head(data3)
# A tibble: 4 x 5
  id                                   filename                          md5                    size state
  <chr>                                <chr>                             <chr>                 <int> <chr>
1 5a65dfb0-dfe8-409a-9f69-6422be7fbbe4 9235a5b1-2a3b-448b-91c5-59c92180… 45026258818732b5abc… 252037 live 
2 dde6619c-ab39-4b52-931d-4673d7528de9 ae36ca5c-e1eb-4a54-a90a-7d69a13f… 3600b6ce959fb0349b6… 246131 live 
3 095f8ccb-1b99-40c0-87b9-4eb3e2a939b4 0cfeaebb-ab33-4711-9c86-f1511004… cc78c5b277095b7435b… 245764 live 
4 e3364a1c-04f5-465c-9979-480a08410c3e 4d0f4fee-5ce4-4124-a602-baff910e… 2a70462dcf2fb3711c4… 251187 live

I want something lik this

34C39A6B-DB6A-47E5-B0D4-5FA990EF7EB8 file id ....

[LiNk-NY]

Hi @bioinfo-dirty-jobs I think you could just use the UUIDtoUUID function in TCGAutils. This Bioconductor package will give you the output you're looking for with an input vector of case UUIDs.

Make sure you're using the devel version of TCGAutils which can also be found on WaldronLab/TCGAutils.

Regards, Marcel

[seandavi]

Thx, @LiNk-NY .