downloadExpData: 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 expression data obtained via RNA-Seq for a given cohort of patients available within The Cancer Genome Atlas project.

Usage

downloadExpData(
  projectID,
  data.dir = "./dataDownload",
  PreProc_cor.cut = 0.6,
  Filt_method = "quantile",
  Filt_qnt.cut = 0.25
)

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"
PreProc_cor.cut	threshold to filter samples according their spearman correlation in samples by samples, numeric in the range 0-1, default: 0.6
Filt_method	method of filtering, available: 'quantile', 'varFilter'
Filt_qnt.cut	threshold selected as mean for filtering, numeric in the range 0-1, default: 0.25

Value

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

Examples

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

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