downloadTcgaData: Fetch genomic datasets based on the given cancer types.

In lihuamei/Biotools: Bioinformatics tools for data analysis.

Description

Fetch the genomic datasets for the given cancer type from TCGA database using the package 'TCGAbiolinks'. All cancer type names can be obtained from https://bioconductor.org/packages/release/bioc/html/TCGAbiolinks.html.

Usage

downloadTcgaData(
  cancerTypes = getGDCprojects()$project_id[grepl("TCGA", getGDCprojects()$project_id)],
  keep = FALSE,
  ...
)

Arguments

cancerTypes	Specify the cancer types for downloading the genimic datasets from the TCGA database.
keep	Keep downloaded files and directories or not, default: FALSE.
...	Other parameters can be obtained through GDCquery functions.

Value

A list of download datasets for the given cancer types. * 'data' - Fetched data matrix. * 'clinical' - Clinical information corressponding to the cancer type.

Examples

results <- downloadTcgaData(cancerTypes = c('TCGA-GBM'), data.category = 'Gene expression', data.type = 'Gene expression quantification', platform = 'Illumina HiSeq', file.type  = 'normalized_results', experimental.strategy = 'RNA-Seq', legacy = TRUE)

lihuamei/Biotools documentation built on July 15, 2020, 1:50 a.m.