curateGSE: Run all steps to download, preprocess and annotate a GEO...

In mensxmachina/BioDataome: Functions used to preprocess datasets stored in BioDataome

Description

Given a GSE id this function downloads, preprocesses, annotates a study and also creates the sample phenotype metadata.

Usage

curateGSE(x, y, z = getwd(), keepRaw = FALSE)

Arguments

x	a GSE series ID
y	a GEO technology id (GPL)
z	the path to save the downloaded files. By default this value is set to the working directory.
keepRaw	keep or not the raw CEL files. By default curateGSE does not keep the raw CEL files.

Value

a list with three components:

• "metadata"a data frame of the metadata with sample phenotype information

• "dataNorm"a numeric matrix of the preprocessed data with variables (probes) as rows and samples as columns

Examples

## Not run: 
curateGSE("GSE11761","GPL570",getwd()) 
## End(Not run)
curatedGSE<-list(metadata=BioDataome:::meta11761,dataNorm=BioDataome:::GSE11761)

mensxmachina/BioDataome documentation built on July 24, 2021, 1:05 p.m.