In waldronlab/MultiAssayExperiment.TCGA: Pipeline for the integration of multi-omics experiments in Bioconductor

knitr::opts_chunk$set(echo = TRUE, eval = FALSE)

library(MultiAssayExperiment.TCGA)
library(BiocParallel)
Sys.setenv(R_DEFAULT_INTERNET_TIMEOUT = 300)
params <- MulticoreParam(
    workers = 34, stop.on.error = FALSE, progressbar = TRUE,
    jobname = "MAEPipeline"
)
TCGAcodes <- getDiseaseCodes()

Create all directories needed in repository

dataDirectories(create = TRUE)

Download all available resources

getClinicalData(TCGAcodes = TCGAcodes, nworkers = 34)
downloadExtraClinical(TCGAcodes = TCGAcodes)

Download SubType data from DropBox

Note. Authentication required using rdrop2

ALTERNATIVELY: You can download files manually and put them in inst/extdata/allsubtypes

## Authenticate to Dropbox API at FIRST RUN
# drop_auth()
# drop_acc() %>% select(uid, display_name, email_verified, quota_info.quota)

downloadSubtypeDrop(TCGAcodes = TCGAcodes)

Merge curated data to clinical data

mergeSubtypeCuration(TCGAcodes = TCGAcodes)

Clean merged data files

cleanMerged(TCGAcodes = TCGAcodes, runDate = "20160128", nworkers = 34)

Build and upload MultiAssayExperiment data

setwd("~/gh/MultiAssayExperiment.TCGA")
res <- bptry({
    bplapply(X = TCGAcodes, FUN = function(cancer) {
        buildMultiAssayExperiment(
            TCGAcode = cancer,
            dataType = c("miRNASeqGene", "RNASeq2GeneNorm"),
            version = "2.1.0",
            upload = TRUE,
            uploadFolder = "staginghub",
            update = TRUE,
            forceDownload = TRUE,
            force = TRUE,
            include = "metadata"
        )
    }, BPPARAM = params)
})

Version 2.1.0

• Includes updates to miRNASeqGene and RNASeq2GeneNorm

res <- bptry({
    bplapply(X = TCGAcodes, FUN = function(cancer) {
        buildMultiAssayExperiment(
            cancer,
            dataType = c("miRNASeqGene", "RNASeq2GeneNorm"),
            version = "2.1.0",
            upload = TRUE,
            uploadFolder = "staginghub",
            update = TRUE,
            forceDownload = TRUE,
            force = TRUE,
            include = "metadata"
        )
    }, BPREDO = res, BPPARAM = params)
})

Version 2.1.1

• Update colData objects with the appropriate subtype curation data

res <- bptry({
    bplapply(X = c("OV", "SKCM"), FUN = function(cancer) {
        buildMultiAssayExperiment(
            TCGAcode = cancer,
            dataType = NULL,
            version = "2.1.1",
            upload = FALSE,
            uploadFolder = "staginghub",
            update = TRUE,
            include = "colData"
        )
    }, BPPARAM = params)
})

waldronlab/MultiAssayExperiment.TCGA documentation built on May 19, 2023, 6:06 p.m.