GEO_Download_GeneExpression: The GEO_Download_GeneExpression function

In gevaertlab/EpiMix: EpiMix: an integrative tool for the population-level analysis of DNA methylation

The GEO_Download_GeneExpression function

Description

Download the gene expression data and the associated sample phenotypic data from the GEO database.

Usage

GEO_Download_GeneExpression(
  AccessionID,
  targetDirectory = ".",
  DownloadData = TRUE
)

Arguments

AccessionID	character string indicating the GEO accession number. Currently support the GEO series (GSE) data type.
targetDirectory	character string indicting the file path to save the data. Default: '.' (current directory)
DownloadData	logical indicating whether the actual data should be downloaded (Default: TRUE). If False, the desired directory where the downloaded data should have been saved is returned.

Value

a list with two elements. The first element ('$GeneExpressionData') indicating the file path to the downloaded methylation data. The second element ('$PhenotypicData') indicating the file path to the sample phenotypic data.

Examples

GEdirectories <- GEO_Download_GeneExpression(AccessionID = 'GSE114065',
                                             targetDirectory = tempdir())

gevaertlab/EpiMix documentation built on July 20, 2023, 9:28 a.m.