TCGAbiolinks

#source("https://bioconductor.org/biocLite.R")
#biocLite("TCGAbiolinks")

library(TCGAbiolinks)
library(data.table)
library(dplyr)
library(DT)

############################################################
# Clinical data 
#
# available clinical info; admin,aliquot,analyte,bio_patient,drug,
#                          follow_up,msi,new_tumor_event,patient,
#                          portion,protocol,radiation,sample,slide,stage_event
#
query <- GDCquery(project = "TCGA-HNSC", 
                  data.category = "Clinical")
                  
GDCdownload(query, method = "api", files.per.chunk = 5)

clinical <- GDCprepare_clinic(query,
                              clinical.info = "patient")

write.csv(clinical,"~/Desktop/TCGA-HNSC.clinical.csv")

###########################################################
# Gene expression data for Lung cancer (LUAD, LUSC)
#
query.LUSC <- GDCquery(project = c("TCGA-LUSC"), 
                  data.category="Transcriptome Profiling",
                  data.type="Gene Expression Quantification",
                  workflow.type="HTSeq - Counts",
                  sample.type=c("Primary solid Tumor","Solid Tissue Normal")) 

GDCdownload(query.LUSC, method = "api", files.per.chunk = 5)

dta.exp.LUSC <- GDCprepare(query.LUSC, save=TRUE,
                           save.filename="LUSC_geneExp_dataframe.rda",
                           summarizedExperiment=TRUE)

geneExp <- SummarizedExperiment::assay(dta.exp.LUSC)

write.csv(geneExp,"/home/bio0/00-NGS/SETDB1_TCGA/exp.LUSC.counts.csv")

###########################################################
# CNV data for Lung cancer (LUAD, LUSC)
#
query.lung.cnv <- GDCquery(project = c("TCGA-LUAD","TCGA-LUSC"), 
                       data.category="Copy Number Variation",
                       data.type="Masked Copy Number Segment",
                       sample.type=c("Primary solid Tumor","Solid Tissue Normal")) 

GDCdownload(query.lung.cnv, method = "api", files.per.chunk = 5)

dta.CNV.LUNG <- GDCprepare(query.lung.cnv, save=TRUE, 
                           save.filename="Lung_CNV_dataframe.rda")

write.csv(dta.CNV.LUNG,"/home/bio0/00-NGS/COSMIC_SETDB1/CNV.LUNG.csv")

###########################################################
# DNA met for Lung cancer (LUAD, LUSC)
#
query.LUAD.met <- GDCquery(project = c("TCGA-LUAD"), legacy = F,
                           data.category="DNA Methylation",
                           platform="Illumina Human Methylation 450",
                           sample.type=c("Primary solid Tumor","Solid Tissue Normal")) 

GDCdownload(query.LUAD.met, method = "api", files.per.chunk = 5)

dta.LUAD.met <- GDCprepare(query.LUAD.met, save=TRUE, 
                           save.filename="Lung_Met_dataframe.rda")

write.csv(dta.LUAD.met,"/home/bio0/00-NGS/COSMIC_SETDB1/LUAD.DNAmet.csv")