R/linkedOmics.R

In BioinformaticsFMRP/TCGAbiolinks: TCGAbiolinks: An R/Bioconductor package for integrative analysis with GDC data

#' @title Retrieve linkedOmics data
#' @description Retrieve linkedOmics data from http://linkedomics.org/
#' @param project A linkedOmics project:
#' \itemize{
#' \item{TCGA-ACC}
#' \item{TCGA-BLCA}
#' \item{TCGA-BRCA}
#' \item{TCGA-CESC}
#' \item{TCGA-CHOL}
#' \item{TCGA-COADREAD}
#' \item{TCGA-DLBC}
#' \item{TCGA-ESCA}
#' \item{TCGA-GBM}
#' \item{TCGA-GBMLGG}
#' \item{TCGA-HNSC}
#' \item{TCGA-KICH}
#' \item{TCGA-KIPAN}
#' \item{TCGA-KIRC}
#' \item{TCGA-KIRP}
#' \item{TCGA-LAML}
#' \item{TCGA-LGG}
#' \item{TCGA-LIHC}
#' \item{TCGA-LUAD}
#' \item{TCGA-LUSC}
#' \item{TCGA-MESO}
#' \item{TCGA-OV}
#' \item{TCGA-PAAD}
#' \item{TCGA-PCPG}
#' \item{TCGA-PRAD}
#' \item{TCGA-SARC}
#' \item{TCGA-SKCM}
#' \item{TCGA-STAD}
#' \item{TCGA-STES}
#' \item{TCGA-TGCT}
#' \item{TCGA-THCA}
#' \item{TCGA-THYM}
#' \item{TCGA-UCEC}
#' \item{TCGA-UCS}
#' \item{TCGA-UVM}
#' \item{CPTAC-COAD}
#' }
#' @param dataset A dataset from the list below
#' \itemize{
#' \item{ Annotated mutation }
#' \item{ Clinical }
#' \item{ Glycoproteome (Gene level) }
#' \item{ Glycoproteome (Site level) }
#' \item{ Methylation (CpG-site level, HM27) }
#' \item{ Methylation (CpG-site level, HM450K) }
#' \item{ Methylation (Gene level, HM27) }
#' \item{ Methylation (Gene level, HM450K) }
#' \item{ miRNA (GA, Gene level) }
#' \item{ miRNA (GA, Isoform level) }
#' \item{ miRNA (GA, miRgene level) }
#' \item{ miRNA (Gene level) }
#' \item{ miRNA (HiSeq, Gene level) }
#' \item{ miRNA (HiSeq, miRgene level) }
#' \item{ miRNA (isoform level) }
#' \item{ miRNA (miRgene level) }
#' \item{ Mutation (Gene level) }
#' \item{ Mutation (Site level) }
#' \item{ Mutation raw file (Somatic and MSIndel) }
#' \item{ Phosphoproteome (Gene level) }
#' \item{ Phosphoproteome (Site level) }
#' \item{ Phosphoproteomics (Normal) }
#' \item{ Phosphoproteomics (Tumor) }
#' \item{ Proteome (Gene level) }
#' \item{ Proteome (Gene Level) }
#' \item{ Proteome (JHU, Gene level) }
#' \item{ Proteome (PNNL, Gene level, Normal TMT Unshared Log Ratio) }
#' \item{ Proteome (PNNL, Gene level, Tumor TMT Unshared Log Ratio) }
#' \item{ Proteome (PNNL, Gene level) }
#' \item{ Proteome (VU, Gene level, Label-free Unshared Counts) }
#' \item{ RNAseq (GA, Gene level) }
#' \item{ RNAseq (HiSeq, Gene level) }
#' \item{ RPPA (Analyte level) }
#' \item{ RPPA (Analyte Level) }
#' \item{ RPPA (Gene level) }
#' \item{ RPPA (Gene Level) }
#' \item{ SCNV (Focal level, log-ratio) }
#' \item{ SCNV (Focal level, Thresholded) }
#' \item{ SCNV (Gene level, log ratio) }
#' \item{ SCNV (Gene level, log-ratio) }
#' \item{ SCNV (Gene level, Thresholded) }
#' \item{ SCNV (Segment level) }
#' }
#' @export
#' @return A matrix with the data
#' @examples
#' \dontrun{
#' TCGA_COAD_protein <- getLinkedOmicsData(
#'   project = "TCGA-COADREAD",
#'   dataset = "Proteome (Gene level)"
#' )
#' TCGA_COAD_RNASeq_hiseq <- getLinkedOmicsData(
#'   project = "TCGA-COADREAD",
#'   dataset = "RNAseq (HiSeq, Gene level)"
#' )
#' TCGA_COAD_RNASeq_ga <- getLinkedOmicsData(
#'   project = "TCGA-COADREAD",
#'   dataset = "RNAseq (GA, Gene level)"
#' )
#' TCGA_COAD_RPPA <- getLinkedOmicsData(
#'   project = "TCGA-COADREAD",
#'   dataset = "RPPA (Gene level)"
#' )
#' }
getLinkedOmicsData <- function(project, dataset){

    tab <- get(data("linkedOmics.data",package = "TCGAbiolinksGUI.data", envir = environment()))

    if(missing(project) || !project %in% tab$project){
        print(knitr::kable(data.frame("Avail projects" = tab$project %>% unique())))
        stop("Project not found! Possible list is above")
    }
    tab <- tab %>% dplyr::filter(.data$project == !!project)

    if(missing(dataset) || !dataset %in% tab$`OMICS Dataset`){
        print(knitr::kable(data.frame("Avail dataset" = tab$`OMICS Dataset` %>% unique())))
        stop("dataset not found! Possible list is above")
    }
    tab <- tab %>% dplyr::filter(.data$`OMICS Dataset` == !!dataset)
    url <- tab %>% pull("url")
    readr::read_tsv(url,col_types = readr::cols())
}