TCGAprepare: Read the data from level 3 the experiments and prepare it for downstream analysis into a SummarizedExperiment object.

Description

This function will read the data from level 3 the experiments and prepare it for downstream analysis into a SummarizedExperiment object.

The samples are always refered by their barcode.

If you want to save the data into an rda file, please use the save parameter that will save an rda object with the filename parameter. If no filename was set, the filename will be the concatenation of platform and Sys.time.

List of accepted platforms:

AgilentG4502A_07_1/AgilentG4502A_07_2/AgilentG4502A_07_3
Genome_Wide_SNP_6
H-miRNA_8x15K/H-miRNA_8x15Kv2
HG-U133_Plus_2
HT_HG-U133A
HumanMethylation27
HumanMethylation450
IlluminaDNAMethylation_OMA002_CPI
IlluminaDNAMethylation_OMA003_CPI
IlluminaGA_RNASeq
IlluminaGA_RNASeqV2
IlluminaHiSeq_RNASeq
IlluminaHiSeq_RNASeqV2
IlluminaHiSeq_TotalRNASeqV2

ReturnThe default output is a SummarizedExperiment object.

Usage

TCGAprepare(query, dir = NULL, samples = NULL, type = NULL, save = FALSE, filename = NULL, add.mutation.genes = FALSE, add.clinical = TRUE, reannotate = FALSE, summarizedExperiment = TRUE, add.subtype = FALSE)

Arguments

query

TCGAquery output

dir

Directory with the files downloaded by TCGAdownload

samples

List of samples to prepare the data

type

Filter the files to prepare.

save

Save a rda object with the prepared object? Default: FALSE

filename

Name of the saved file

add.mutation.genes

Integrate information about genes mutation? DEFAULT: FALSE

add.clinical

Add clinical information from TCGAquery_clinic? (The information file add will be: clinical_patient) Default: FALSE

reannotate

Reannotate genes? Source http://grch37.ensembl.org/. DEFAULT: FALSE. (For the moment only working for methylation data)

summarizedExperiment

Output as SummarizedExperiment? Default: FALSE

add.subtype

Add subtype information from tcgaquery_subtype? Default: FALSE

Value

A SummarizedExperiment object (If SummarizedExperiment = FALSE, a data.frame)

Examples

Run this code

sample <- "TCGA-06-0939-01A-01D-1228-05"
query <- TCGAquery(tumor = "GBM",samples = sample, level = 3)
TCGAdownload(query,path = "exampleData",samples = sample)
data <- TCGAprepare(query, dir="exampleData")

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