Load GEO Dataset from SOFT File

Imports a GEO dataset and converts it into a structured ExpressionSet object. If a local SOFT file is found at file.path it is loaded directly. Otherwise the dataset is downloaded from NCBI GEO using accession and cached in tempdir().

Usage

load.geo.soft(file.path = NULL, accession = NULL, log.transform = FALSE)

Arguments

file.path

Character. Path to a local GEO SOFT file. If the file does not exist and accession is provided, the dataset is downloaded automatically.

accession

Character. GEO accession ID (e.g., "GDS507"). Only used when file.path does not exist. Default is NULL.

log.transform

Logical. Whether to apply a log2 transformation to the expression matrix during import. Default is FALSE.

Value

An ExpressionSet object for use with extract.expression().

Examples

# \donttest{
# Download automatically if not found locally
eset <- load.geo.soft("GDS507.soft", accession = "GDS507", log.transform = TRUE)
#> GDS507 not found locally, downloading from NCBI GEO...
#> Using locally cached version of GDS507 found here:
#> /tmp/RtmpxRZSjV/GDS507.soft.gz 
#> Using locally cached version of GPL97 found here:
#> /tmp/RtmpxRZSjV/GPL97.annot.gz 

# Download without a local file at all
eset <- load.geo.soft(NULL, accession = "GDS507", log.transform = TRUE)
#> GDS507 not found locally, downloading from NCBI GEO...
#> Using locally cached version of GDS507 found here:
#> /tmp/RtmpxRZSjV/GDS507.soft.gz 
#> Using locally cached version of GPL97 found here:
#> /tmp/RtmpxRZSjV/GPL97.annot.gz 
# }