getTCGA: getTCGA to download DNA methylation, RNA expression and...

In ELMER: Inferring Regulatory Element Landscapes and Transcription Factor Networks Using Cancer Methylomes

Description

getTCGA is a function to download DNA methylation, RNA expression and clinic data for all samples of certain cancer type from TCGA website. And downloaded data will be transform to matrixes or data frame for further analysis.

Usage

getTCGA(disease, Meth=TRUE, RNA=TRUE, Clinic=TRUE, basedir="./Data", genome = "hg38")

Arguments

disease	A character specifies the disease to download in TCGA such as BLCA
Meth	A logic if TRUE HM450K DNA methylation data will download.
RNA	A logic if TRUE RNA-seq Hiseq-V2 from TCGA level 3 will be download.
Clinic	A logic if TRUE clinic data will be download for that disease.
basedir	A path shows where the data will be stored.
genome	Data aligned against which genome of reference. Options: "hg19", "hg38" (default)

Value

Download DNA methylation (HM450K)/RNAseq(HiseqV2)/Clinic data for the specified disease from TCGA.

Examples

getTCGA(disease = "BRCA",
        Meth = FALSE, 
        RNA = FALSE, 
        Clinic = TRUE, 
        basedir = tempdir(), 
        genome = "hg19"
        )

ELMER documentation built on Nov. 8, 2020, 4:59 p.m.