inst/scripts/miniACC-Ex.R

In vjcitn/MultiAssayExperiment: Software for the integration of multi-omics experiments in Bioconductor

##
## The following is the code used to create this mini dataset from the full ACC dataset.
## The full ACC MultiAssayExperiment was created by the pipeline at
## https://github.com/waldronlab/multiassayexperiment-tcga.
\dontrun{
    ## See www.tinyurl.com/MAEOurls for more pre-built TCGA MultiAssayExperiment objects
    download.file("http://s3.amazonaws.com/multiassayexperiments/accMAEO.rds",
                  destfile = "accMAEO.rds")
    library(MultiAssayExperiment)
    library(RaggedExperiment) #needed for RaggedExperiment objects by updateObject()
    library(Biobase)

    acc <- readRDS("accMAEO.rds")
    acc <- updateObject(acc)
    protmap <- read.csv(paste0("http://genomeportal.stanford.edu/",
                        "pan-tcga/target_selection_send_data",
                        "?filename=Allprotein.txt"), as.is = TRUE
        )

    RPPAgenes <- Filter(function(x) x != "", protmap$Genes)
    RPPAgenes <- unlist(strsplit(RPPAgenes, ","))
    RPPAgenes <- unique(RPPAgenes)

    miniACC <-
        acc[RPPAgenes, , c("RNASeq2GeneNorm", "gistict", "RPPAArray", "Mutations")]
    mut <- assay(miniACC[["Mutations"]], i = "Variant_Classification")
    mut <- ifelse(is.na(mut) | mut == "Silent", 0, 1)

    miniACC[["Mutations"]] <- mut
    colData(miniACC) <- colData(miniACC)[, c(1:17, 810:822)]

    rpparowData <-
        protmap[match(rownames(miniACC[["RPPAArray"]]), protmap$Genes),]
    rpparowData <- AnnotatedDataFrame(rpparowData)
    featureData(miniACC[["RPPAArray"]]) <- rpparowData

    md <-
        list(
            title = "Comprehensive Pan-Genomic Characterization of Adrenocortical Carcinoma",
            PMID = "27165744",
            sourceURL = "http://s3.amazonaws.com/multiassayexperiments/accMAEO.rds",
            RPPAfeatureDataURL = paste0("http://genomeportal.stanford.edu/",
                                        "pan-tcga/show_target_selection_file",
                                        "?filename=Allprotein.txt"),
            colDataExtrasURL = "http://www.cell.com/cms/attachment/2062093088/2063584534/mmc3.xlsx"
        )
    metadata(miniACC) <- md

    mirna <- acc[["miRNASeqGene"]]
    mirna <- mirna[rowSums(assay(mirna) >= 5) >= 5, ]
    experimentData(mirna)@abstract <-
        "Note: Rows not having at least 5 counts in at least 5 samples were removed."
    miniACC <- c(miniACC,
                 list(miRNASeqGene = mirna),
                 sampleMap = sampleMap(acc)[sampleMap(acc)$assay == "miRNASeqGene",])

     miniACC[["RNASeq2GeneNorm"]] <-
         as(miniACC[["RNASeq2GeneNorm"]], "SummarizedExperiment")
     miniACC[["RPPAArray"]] <-
         as(miniACC[["RPPAArray"]], "SummarizedExperiment")
     miniACC[["miRNASeqGene"]] <-
         as(miniACC[["miRNASeqGene"]], "SummarizedExperiment")

    save(miniACC, file = "data/miniACC.RData", compress = "bzip2")
}