load.exp.GEO: Download Gene Expression Series From GEO Database with...

In jyyulab/NetBID: Network-based Bayesian Inference of Drivers, version 2

Download Gene Expression Series From GEO Database with Platform Specified

Description

load.exp.GEO downloads user assigned Gene Expression Series (GSE file) along with its Platform from GEO dataset. It returns an ExpressionSet class object and saves it as RData. If the GSE RData already exists, it will be loaded directly. It also allows users to update the Gene Expression Series RData saved before.

Usage

load.exp.GEO(
  out.dir = NULL,
  GSE = NULL,
  GPL = NULL,
  getGPL = TRUE,
  update = FALSE
)

Arguments

out.dir	character, the file path used to save the GSE RData. If the data already exsits, it will be loaded from this path.
GSE	character, the GEO Series Accession ID.
GPL	character, the GEO Platform Accession ID.
getGPL	logical, if TRUE, the corresponding GPL file will be downloaded. Default is TRUE.
update	logical, if TRUE, the previous stored Gene ExpressionSet RData will be updated. Default is FALSE

Value

Return an ExpressionSet class object.

Examples

## Not run: 
# Download the GSE116028 which performed on GPL6480 platform
# from GEO and save it to the current directory
# Assign this ExpressionSet object to net_eset
net_eset <- load.exp.GEO(out.dir='./',
                         GSE='GSE116028',
                         GPL='GPL6480',
                         getGPL=TRUE,
                         update=FALSE)

## End(Not run)

jyyulab/NetBID documentation built on Dec. 23, 2024, 6:34 a.m.