Date of data generation
Closed this issue · 2 comments
adomingues commented
Hi all,
I am trying to extract the rrpa data for several of the cohorts but noticed in the files names that the data generation time seems a bit old (20160128):
curatedTCGAData("acc", version = "2.1.0")
snapshotDate(): 2023-04-24
See '?curatedTCGAData' for 'diseaseCode' and 'assays' inputs
ah_id title file_size rdataclass rdatadateadded rdatadateremoved
1 EH4737 ACC_CNASNP-20160128 0.8 Mb RaggedExperiment 2021-01-27 <NA>
2 EH4738 ACC_CNVSNP-20160128 0.2 Mb RaggedExperiment 2021-01-27 <NA>
3 EH4740 ACC_GISTIC_AllByGene-20160128 0.2 Mb SummarizedExperiment 2021-01-27 <NA>
4 EH4741 ACC_GISTIC_Peaks-20160128 0 Mb RangedSummarizedExperiment 2021-01-27 <NA>
5 EH4742 ACC_GISTIC_ThresholdedByGene-20160128 0.2 Mb SummarizedExperiment 2021-01-27 <NA>
6 EH4744 ACC_Methylation-20160128_assays 239.2 Mb SummarizedExperiment 2021-01-27 <NA>
7 EH4745 ACC_Methylation-20160128_se 6 Mb RaggedExperiment 2021-01-27 <NA>
8 EH4747 ACC_Mutation-20160128 0.7 Mb SummarizedExperiment 2021-01-27 <NA>
9 EH4748 ACC_RNASeq2Gene-20160128 2.7 Mb SummarizedExperiment 2021-01-27 <NA>
10 EH4750 ACC_RPPAArray-20160128 0.1 Mb SummarizedExperiment 2021-01-27 <NA>
11 EH8118 ACC_miRNASeqGene-20160128 0.2 Mb SummarizedExperiment 2023-04-24 <NA>
12 EH8119 ACC_RNASeq2GeneNorm-20160128 5.4 Mb SummarizedExperiment 2023-04-24 <NA>
So my question is if curatedTCGAData provides access to the latest data available in TCGA (within reason)?
Thank you for proving such a wonderful package!
LiNk-NY commented
Hi @adomingues
It provides data from the GDAC Firehose pipeline whose last run was in 2016. For more recently harmonized data, see the GenomicDataCommons
package and/or https://portal.gdc.cancer.gov/
Best,
Marcel
adomingues commented
Thanks @LiNk-NY! I was already exploring GenomicDataCommons
and have a question about it, but I will use the bioconductor forum for that