## ----setup, include=FALSE----------------------------------------------------- knitr::opts_chunk$set(echo = TRUE) knitr::opts_knit$set(progress = FALSE) ## ----message=FALSE, warning=FALSE, include=FALSE------------------------------ library(TCGAbiolinks) library(SummarizedExperiment) library(dplyr) library(DT) ## ----BCR_Biotab, results='hide', echo=TRUE, message=FALSE, warning=FALSE------ query <- GDCquery( project = "TCGA-ACC", data.category = "Clinical", data.type = "Clinical Supplement", data.format = "BCR Biotab" ) GDCdownload(query) clinical.BCRtab.all <- GDCprepare(query) names(clinical.BCRtab.all) ## ----echo=TRUE, message=FALSE, warning=FALSE---------------------------------- clinical.BCRtab.all$clinical_drug_acc %>% head %>% DT::datatable(options = list(scrollX = TRUE, keys = TRUE)) ## ----results = "hide",cache=TRUE, message=FALSE------------------------------- library(TCGAbiolinks) query <- GDCquery( project = "TCGA-ACC", data.category = "Clinical", data.type = "Clinical Supplement", data.format = "BCR Biotab" ) GDCdownload(query) clinical_tab_all <- GDCprepare(query) ## ----------------------------------------------------------------------------- # All available tables names(clinical_tab_all) # columns from clinical_patient dplyr::glimpse(clinical_tab_all$clinical_patient_acc) ## ----results = "hide",cache=TRUE, message=FALSE,warning=FALSE----------------- # Biospecimen BCR Biotab query_biospecimen <- GDCquery( project = "TCGA-ACC", data.category = "Biospecimen", data.type = "Biospecimen Supplement", data.format = "BCR Biotab" ) GDCdownload(query_biospecimen) biospecimen_tab_all <- GDCprepare(query_biospecimen) ## ----------------------------------------------------------------------------- # All available tables names(biospecimen_tab_all) biospecimen_tab_all$biospecimen_sample_acc %>% head %>% DT::datatable(options = list(scrollX = TRUE, keys = TRUE)) ## ----results='hide', echo=TRUE, message=FALSE, warning=FALSE------------------ clinical <- GDCquery_clinic(project = "TCGA-ACC", type = "clinical") ## ----echo=TRUE, message=FALSE, warning=FALSE---------------------------------- clinical %>% head %>% DT::datatable( filter = 'top', options = list(scrollX = TRUE, keys = TRUE, pageLength = 5), rownames = FALSE ) ## ----eval=FALSE,results='hide', echo=TRUE, message=FALSE, warning=FALSE------- # clinical_beataml <- GDCquery_clinic( # project = "BEATAML1.0-COHORT", # type = "clinical" # ) # # clinical_cptac2 <- GDCquery_clinic( # project = "CPTAC-2", # type = "clinical" # ) # # clinical_genie <- GDCquery_clinic( # project = "GENIE-MSK", # type = "clinical" # ) ## ----results = 'hide',echo=TRUE, message=FALSE, warning=FALSE----------------- query <- GDCquery( project = "TCGA-COAD", data.category = "Clinical", data.format = "bcr xml", barcode = c("TCGA-RU-A8FL","TCGA-AA-3972") ) GDCdownload(query) clinical <- GDCprepare_clinic(query, clinical.info = "patient") ## ----echo = TRUE, message = FALSE, warning = FALSE---------------------------- clinical %>% datatable(filter = 'top', options = list(scrollX = TRUE, keys = TRUE, pageLength = 5), rownames = FALSE) ## ----results = 'hide', echo=TRUE, message=FALSE, warning=FALSE---------------- clinical.drug <- GDCprepare_clinic(query, clinical.info = "drug") ## ----echo = TRUE, message = FALSE, warning = FALSE---------------------------- clinical.drug %>% datatable(filter = 'top', options = list(scrollX = TRUE, keys = TRUE, pageLength = 5), rownames = FALSE) ## ----results = 'hide', echo=TRUE, message=FALSE, warning=FALSE---------------- clinical.radiation <- GDCprepare_clinic(query, clinical.info = "radiation") ## ----echo = TRUE, message = FALSE, warning = FALSE---------------------------- clinical.radiation %>% datatable(filter = 'top', options = list(scrollX = TRUE, keys = TRUE, pageLength = 5), rownames = FALSE) ## ----results = 'hide', echo=TRUE, message=FALSE, warning=FALSE---------------- clinical.admin <- GDCprepare_clinic(query, clinical.info = "admin") ## ----echo = TRUE, message = FALSE, warning = FALSE---------------------------- clinical.admin %>% datatable(filter = 'top', options = list(scrollX = TRUE, keys = TRUE, pageLength = 5), rownames = FALSE) ## ----results = 'hide', echo=TRUE, message=FALSE, warning=FALSE---------------- # Pathology report from harmonized portal query_harmonized <- GDCquery( project = "TCGA-COAD", data.category = "Biospecimen", data.type = "Slide Image", experimental.strategy = "Diagnostic Slide", barcode = c("TCGA-RU-A8FL","TCGA-AA-3972") ) ## ----echo=TRUE, message=FALSE, warning=FALSE---------------------------------- query_harmonized %>% getResults %>% head %>% DT::datatable(options = list(scrollX = TRUE, keys = TRUE)) ## ----eval = TRUE-------------------------------------------------------------- bar <- c( "TCGA-G9-6378-02A-11R-1789-07", "TCGA-CH-5767-04A-11R-1789-07", "TCGA-G9-6332-60A-11R-1789-07", "TCGA-G9-6336-01A-11R-1789-07", "TCGA-G9-6336-11A-11R-1789-07", "TCGA-G9-7336-11A-11R-1789-07", "TCGA-G9-7336-04A-11R-1789-07", "TCGA-G9-7336-14A-11R-1789-07", "TCGA-G9-7036-04A-11R-1789-07", "TCGA-G9-7036-02A-11R-1789-07", "TCGA-G9-7036-11A-11R-1789-07", "TCGA-G9-7036-03A-11R-1789-07", "TCGA-G9-7036-10A-11R-1789-07", "TCGA-BH-A1ES-10A-11R-1789-07", "TCGA-BH-A1F0-10A-11R-1789-07", "TCGA-BH-A0BZ-02A-11R-1789-07", "TCGA-B6-A0WY-04A-11R-1789-07", "TCGA-BH-A1FG-04A-11R-1789-08", "TCGA-D8-A1JS-04A-11R-2089-08", "TCGA-AN-A0FN-11A-11R-8789-08", "TCGA-AR-A2LQ-12A-11R-8799-08", "TCGA-AR-A2LH-03A-11R-1789-07", "TCGA-BH-A1F8-04A-11R-5789-07", "TCGA-AR-A24T-04A-55R-1789-07", "TCGA-AO-A0J5-05A-11R-1789-07", "TCGA-BH-A0B4-11A-12R-1789-07", "TCGA-B6-A1KN-60A-13R-1789-07", "TCGA-AO-A0J5-01A-11R-1789-07", "TCGA-AO-A0J5-01A-11R-1789-07", "TCGA-G9-6336-11A-11R-1789-07", "TCGA-G9-6380-11A-11R-1789-07", "TCGA-G9-6380-01A-11R-1789-07", "TCGA-G9-6340-01A-11R-1789-07", "TCGA-G9-6340-11A-11R-1789-07" ) S <- TCGAquery_SampleTypes(bar,"TP") S2 <- TCGAquery_SampleTypes(bar,"NB") # Retrieve multiple tissue types NOT FROM THE SAME PATIENTS SS <- TCGAquery_SampleTypes(bar,c("TP","NB")) # Retrieve multiple tissue types FROM THE SAME PATIENTS SSS <- TCGAquery_MatchedCoupledSampleTypes(bar,c("NT","TP")) ## ----eval = FALSE------------------------------------------------------------- # # This code will get all clinical indexed data from TCGA # library(data.table) # library(dplyr) # library(regexPipes) # clinical <- TCGAbiolinks:::getGDCprojects()$project_id %>% # regexPipes::grep("TCGA",value = TRUE) %>% # sort %>% # plyr::alply(1,GDCquery_clinic, .progress = "text") %>% # rbindlist # readr::write_csv(clinical,path = paste0("all_clin_indexed.csv")) # # # This code will get all clinical XML data from TCGA # getclinical <- function(proj){ # message(proj) # while(1){ # result = tryCatch({ # query <- GDCquery(project = proj, data.category = "Clinical",data.format = "bcr xml") # GDCdownload(query) # clinical <- GDCprepare_clinic(query, clinical.info = "patient") # for(i in c("admin","radiation","follow_up","drug","new_tumor_event")){ # message(i) # aux <- GDCprepare_clinic(query, clinical.info = i) # if(is.null(aux) || nrow(aux) == 0) next # # add suffix manually if it already exists # replicated <- which(grep("bcr_patient_barcode",colnames(aux), value = T,invert = T) %in% colnames(clinical)) # colnames(aux)[replicated] <- paste0(colnames(aux)[replicated],".",i) # if(!is.null(aux)) clinical <- merge(clinical,aux,by = "bcr_patient_barcode", all = TRUE) # } # readr::write_csv(clinical,path = paste0(proj,"_clinical_from_XML.csv")) # Save the clinical data into a csv file # return(clinical) # }, error = function(e) { # message(paste0("Error clinical: ", proj)) # }) # } # } # clinical <- TCGAbiolinks:::getGDCprojects()$project_id %>% # regexPipes::grep("TCGA",value=T) %>% sort %>% # plyr::alply(1,getclinical, .progress = "text") %>% # rbindlist(fill = TRUE) %>% setDF %>% subset(!duplicated(clinical)) # # readr::write_csv(clinical,path = "all_clin_XML.csv") # # result: https://drive.google.com/open?id=0B0-8N2fjttG-WWxSVE5MSGpva1U # # Obs: this table has multiple lines for each patient, as the patient might have several followups, drug treatments, # # new tumor events etc...