Get all TCGA data for GENAVi https://junkdnalab.shinyapps.io/GENAVi/

GENAVi_input.R

library(TCGAbiolinks)
library(SummarizedExperiment)
dir.create(gsub(" |,", "_",TCGAbiolinks:::getGDCInfo()$data_release))
setwd(gsub(" |,", "_",TCGAbiolinks:::getGDCInfo()$data_release))
projects <- TCGAbiolinks:::getGDCprojects()$project_id
projects <- projects[grepl('^TCGA',projects,perl=T)]
for(proj in projects){
    dir.create(proj,showWarnings = FALSE)
    query <- GDCquery(project = proj,
                      data.category = "Transcriptome Profiling", 
                      data.type = "Gene Expression Quantification", 
                      workflow.type = "HTSeq - Counts")
    GDCdownload(query)
    data <- GDCprepare(query = query,
                       save = FALSE)
    #saveRDS(data, file = file.path(proj,"/SE_raw_counts_hg38_TCGA.rds"))
    
    df <- as.data.frame(assay(data))
    df <- cbind(rownames(df),df)
    readr::write_csv(df,path = file.path(proj,"/raw_counts_hg38_TCGA.csv"))
    
    samples <- cbind(rownames(colData(data)), colData(data))
    readr::write_csv(as.data.frame(samples),path = file.path(proj,"metadata.csv"))
}