Hello, I am using TCGAbiolinks routinely to analyse molecular abnormalities by using heatmap and survival plots. I use the commands below. For 2 days, TCGAanalyze_survival has given the error below because days_to_death column is missing in expression data downloaded and prepared by GDCquery, GDCdownload and GDCprepare commands. What has changed in two days? How can I solve this problem?

query_exp2 <- GDCquery(project = paste0("TCGA-", cancer),
                       data.category = "Transcriptome Profiling",
                       data.type = "Gene Expression Quantification", 
                       workflow.type = "HTSeq - Counts",
                       sample.type = "Primary solid Tumor",
                       barcode = uniq_tsb_exp)

GDCdownload(query_exp2, files.per.chunk = 100)

GeneExp_paired2 <- GDCprepare(query_exp2, save = TRUE, save.filename = paste0(cancer, "_GeneExp_paired2.rda"))

TCGAanalyze_survival(data = colData(GeneExp_paired2),
                     clusterCol = "subtype_iCluster.Group",
                     main = "TCGA Kaplan-Meier Survival Plot for Consensus Clusters",
                     legend = "RNA Group",
                     height = 10,
                     risk.table = FALSE,
                     conf.int = FALSE,
                     color = c("black","red","blue","green3"),
                     filename = paste0(cancer, "_survival_expression_subtypes0.png"))

Error in TCGAanalyzesurvival(data = colData(GeneExppaired2), clusterCol = "subtypeiCluster.Group", : Columns vitalstatus, daystodeath and daystolastfollowup should be in data frame

I tried the same code for two version of TCGAbiolinks but they gave the same error.

package.version("TCGAbiolinks")
[1] "2.9.2"
GeneExp_paired2$days_to_death
NULL

package.version("TCGAbiolinks")
[1] "2.10.5"
GeneExp_paired2$days_to_death
NULL

I tried to get days_to_death column from clinic data but this column is missing in clinic data, too. The used code is below:

clinic <- GDCquery_clinic(project = paste0("TCGA-", cancer), type = "clinical")
clinic$days_to_death
NULL

Thanks in advance.

There was a bug in GDC API. They are making changes and the data was removed. They fixed and the metadata should be correct.