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
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")  "2.9.2" GeneExp_paired2$days_to_death NULL package.version("TCGAbiolinks")  "2.10.5" GeneExp_paired2$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.