downloadCNVdata: This function downloads, pre-processes and filters harmonized...

In kkolmus/MolecularAnalyzeR: This package aims at checking correlation between gene expression and copy number variation for cohorts of patients analyzed within The Cancer Genome Atlas project

Description

This function downloads, pre-processes and filters harmonized copy number variation data obtained via RNA-Seq for a given cohort of patients available within The Cancer Genome Atlas project.

Usage

downloadCNVdata(projectID, data.dir = "./dataDownload")

Arguments

projectID	cohort of patients in TCGA database, for list available projects type: listTCGAcohorts(), character string
data.dir	directory to save expression data, character string, default: "./dataDownload"

Value

matrix with CNV data; columns are internal patient IDs, rows are HGNC gene symbols

Examples

## Not run: downloadCNVdata(projectID = "TCGA-COAD")

kkolmus/MolecularAnalyzeR documentation built on Dec. 21, 2021, 6:46 a.m.