Download Ovarian Cancer dataset from TCGA

library(TCGAbiolinks)

tumor = "OV"
project = paste0("TCGA-", tumor)
genome = "hg38"

methylation_platforms <- c("Illumina Human Methylation 27",
                           "Illumina Human Methylation 450")

dirname = "downloadTCGA"
if (!file.exists(dirname)){
  dir.create(dirname)
}

Clinical data

cliQuery <- GDCquery(project = project, data.category = "Clinical", 
                     data.format = "bcr xml")
GDCdownload(cliQuery, method="api", files.per.chunk = 10, 
            directory = "downloadTCGA/GDCdata")
followUp <- GDCprepare_clinic(cliQuery, clinical.info = "follow_up",
                              directory = "downloadTCGA/GDCdata")
newTumorEvent <- GDCprepare_clinic(cliQuery, clinical.info = "new_tumor_event",
                                   directory = "downloadTCGA/GDCdata")

Expression

expQuery <- GDCquery(project = project,
                     data.category = "Transcriptome Profiling",
                     data.type = "Gene Expression Quantification",
                     workflow.type = "STAR - Counts")
GDCdownload(expQuery, method = "api", files.per.chunk = 6, 
            directory = "downloadTCGA/GDCdata")
exprData <- GDCprepare(expQuery, directory = "downloadTCGA/GDCdata")

Methylation

metQuery <- GDCquery(project = project,
                     data.category = "DNA Methylation",
                     data.type = "Methylation Beta Value",
                     platform = methylation_platforms)
GDCdownload(metQuery, method = "api", directory = "downloadTCGA/GDCdata")

metQuery27 <- GDCquery(project = project,
                       data.category = "DNA Methylation",
                       data.type = "Methylation Beta Value",
                       platform = methylation_platforms[[1]])
metData27 <- GDCprepare(metQuery27, directory = "downloadTCGA/GDCdata")

metQuery450 <- GDCquery(project = project,
                        data.category = "DNA Methylation",
                        data.type = "Methylation Beta Value",
                        platform = methylation_platforms[[2]])
metData450 <- GDCprepare(metQuery450, directory = "downloadTCGA/GDCdata")

Mutation

mutQuery <- GDCquery(
    project = project, 
    data.category = "Simple Nucleotide Variation", 
    data.type = "Masked Somatic Mutation",
    workflow.type = "Aliquot Ensemble Somatic Variant Merging and Masking")

GDCdownload(mutQuery, method = "api", directory = "downloadTCGA/GDCdata")
mutData <- GDCprepare(mutQuery, directory = "downloadTCGA/GDCdata")

Copy number variation

gisticTable <- getGistic("OV-TP", type = "thresholded")
cnvData <- gisticTable[, -c(1:3)]
colnames(cnvData) <- substr(colnames(cnvData), 1, 12)
row.names(cnvData) <- gisticTable$`Locus ID`

Save downloaded data in .RData file.

save(exprData, metData27, metData450, mutData, cnvData, followUp, newTumorEvent, 
     file = paste0(dirname, '/', project, "-", genome, ".RData"))