## ----message=FALSE, warning=FALSE, include=FALSE------------------------- library(TCGAbiolinks) library(SummarizedExperiment) library(dplyr) library(DT) ## ----results = 'hide', echo=TRUE, message=FALSE, warning=FALSE----------- # Get XML files and parse them clin.query <- GDCquery(project = "TCGA-READ", data.category = "Clinical", barcode = "TCGA-F5-6702") GDCdownload(clin.query) clinical.patient <- GDCprepare_clinic(clin.query, clinical.info = "patient") clinical.patient.followup <- GDCprepare_clinic(clin.query, clinical.info = "follow_up") # Get indexed data clinical.index <- GDCquery_clinic("TCGA-READ") ## ----echo = TRUE, message = FALSE, warning = FALSE----------------------- select(clinical.patient,vital_status,days_to_death,days_to_last_followup) %>% datatable select(clinical.patient.followup, vital_status,days_to_death,days_to_last_followup) %>% datatable # Vital status should be the same in the follow up table filter(clinical.index,submitter_id == "TCGA-F5-6702") %>% select(vital_status,days_to_death,days_to_last_follow_up) %>% datatable ## ----results = 'hide', echo=TRUE, message=FALSE, warning=FALSE----------- # Get XML files and parse them recurrent.samples <- GDCquery(project = "TCGA-LIHC", data.category = "Transcriptome Profiling", data.type = "Gene Expression Quantification", workflow.type = "HTSeq - Counts", sample.type = "Recurrent Solid Tumor")$results[[1]] %>% select(cases) recurrent.patients <- unique(substr(recurrent.samples$cases,1,12)) clin.query <- GDCquery(project = "TCGA-LIHC", data.category = "Clinical", barcode = recurrent.patients) GDCdownload(clin.query) clinical.patient <- GDCprepare_clinic(clin.query, clinical.info = "patient") ## ----echo = TRUE, message = FALSE, warning = FALSE----------------------- # Get indexed data GDCquery_clinic("TCGA-LIHC") %>% filter(submitter_id %in% recurrent.patients) %>% select(progression_or_recurrence,days_to_recurrence,tumor_grade) %>% datatable # XML data clinical.patient %>% select(bcr_patient_barcode,neoplasm_histologic_grade) %>% datatable