barcodeToUUID error: arguments imply differing number of rows

[lwaldron]

Do you know what's going on here? Would be nice to make this work on the subset of mappable barcodes:

suppressPackageStartupMessages(library(ExperimentHub))
eh <- ExperimentHub()
#> snapshotDate(): 2018-08-20
gbmmap <- eh[["EH685"]]
suppressPackageStartupMessages(library(TCGAutils))
TCGAutils::barcodeToUUID(gbmmap$colname, id_type="file_id")
#> Error in data.frame(barcode = if (!length(ids(info))) character(0L) else unlist(id_list), : arguments imply differing number of rows: 8230, 8222
len <- lengths(strsplit(gbmmap$colname, ""))
TCGAutils::barcodeToUUID(gbmmap$colname[len==28], id_type="file_id")
#> Error in data.frame(barcode = if (!length(ids(info))) character(0L) else unlist(id_list), : arguments imply differing number of rows: 8230, 8222

[LiNk-NY]

Hi Levi, @lwaldron It looks like a query like this would return multiple file UUIDs per barcode. If you're just interested in the case UUID you can use id_type=case_id otherwise you'd get a one to many data.frame of results. I'm currently working on a fix for this.

[LiNk-NY]

This should work now:

suppressPackageStartupMessages({
    library(TCGAutils)
    library(ExperimentHub)
})
eh <- ExperimentHub()
#> snapshotDate(): 2019-01-25
gbmmap <- eh[["EH685"]]
#> see ?curatedTCGAData and browseVignettes('curatedTCGAData') for documentation
#> downloading 0 resources
#> loading from cache 
#>     '/home/mr148//.ExperimentHub/685'
head(res <- barcodeToUUID(gbmmap$colname))
#>             submitter_aliquot_ids                          aliquot_ids
#> 7481 TCGA-02-0047-01A-01R-1849-01 95d8884d-0961-4070-be07-55dce4c7bc8f
#> 113  TCGA-02-0055-01A-01R-1849-01 065048d0-ecbf-4de2-b12a-55e52f8d1279
#> 7808 TCGA-02-2483-01A-01R-1849-01 35578669-fb40-49fa-b6b5-3bd0f239fa7e
#> 6776 TCGA-02-2485-01A-01R-1849-01 102a0737-7d27-46b8-a433-4f1bb5300858
#> 8918 TCGA-02-2486-01A-01R-1849-01 92972663-4231-4e24-96d1-23857a445e03
#> 4173 TCGA-06-0125-01A-01R-1849-01 ea85c76f-5334-495d-9615-d3f503c0d088

packageVersion("TCGAutils")
#> [1] '1.3.24'

^{Created on 2019-03-18 by the reprex package (v0.2.1)}