buildMultiAssayExperiment: A unifying pipeline function for building...

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

A unifying pipeline function for building MultiAssayExperiment objects

Description

This is the main function of the package. It brings together all of the exported functions to load, create, and save data objects on ExperimentHub and return documented metadata

Usage

buildMultiAssayExperiment(
  TCGAcode,
  dataType = c("RNASeqGene", "RNASeq2Gene", "RNASeq2GeneNorm", "miRNASeqGene", "CNASNP",
    "CNVSNP", "CNASeq", "CNACGH", "Methylation", "mRNAArray", "miRNAArray", "RPPAArray",
    "Mutation", "GISTIC"),
  runDate = "20160128",
  analyzeDate = "20160128",
  version,
  serialDir = "data/raw",
  outDataDir = "data/bits",
  mapDir = "data/maps",
  upload = FALSE,
  uploadFolder,
  update = TRUE,
  force = FALSE,
  forceDownload = FALSE,
  include = c("colData", "sampleMap", "metadata")
)

Arguments

dataType	A character vector of TCGA assay types
runDate	A single string indicating the Firehose run date, usually '20160128'
analyzeDate	'character(1)' The GDAC Firehose analysis run date, only '20160128' is supported
version	'character(1)' A version string for versioning data runs (such as "1.0.0")
serialDir	The directory corresponding to the serialized data from RTCGAToolbox
outDataDir	'character(1)' The single string indicating piecewise data product save location
mapDir	A single string indicating the directory where sampleMaps are stored from 'saveMapData'
upload	'logical(1)' (default FALSE) Whether to save data products to the cloud infrastructure, namely the Azure Blob Storage location.
uploadFolder	'character(1)' The folder where to upload the data (default "staginghub")
update	'logical(1)' (default TRUE) Whether to update the metadata data from the data pooled by the function
force	(logical) Whether to resave all sample maps to the map directory
forceDownload	'logical(1)' Whether to re-download existing resources that were previously saved as Rds files in 'saveRTCGAdata' (default FALSE)
include	'character()' A vector of metadata names to include. It must include any or all of "colData", "sampleMap", or "metadata". This allows to only publish changed data.
TCGAcodes	'character(1)' A single TCGA cancer code

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