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Retrieve GEO SOFT file from NCBI GEO

Source: R/geo-soft.R
geo_soft.Rd

By default, this function uses the soft format for GDS and GSE entities, and the full amount of text format data for GPL and GSM entities.

Usage

geo_soft(
  accession,
  famount = NULL,
  scope = NULL,
  ftp_over_https = NULL,
  handle_opts = list(),
  odir = getwd()
)

Arguments

accession

A character of GEO accession IDs. Examples:

  • DataSets (GDS): "GDS505", "GDS606", "GDS1234", "GDS9999", etc.

  • Series (GSE): "GSE2", "GSE22", "GSE100", "GSE2000", etc.

  • Platforms (GPL): "GPL96", "GPL570", "GPL10558", etc.

  • Samples (GSM): "GSM12345", "GSM67890", "GSM112233", etc.

famount

A character specifying either:

  • the file format on the GEO FTP server, or

  • the amount of data in the GEO Accession Display Bar.

See geo_url() for details on the format and amount arguments.

scope

A character specifying which GEO accessions to include (Only applicable to Accession Display Bar access).

  • "none": Applicable only to DataSets; for DataSets, this is also the sole valid option

  • "self": the queried accession only.

  • "gsm", "gpl", "gse": related samples, platforms, or series.

  • "all": all accessions related to the query (family view).

ftp_over_https

Logical scalar. If TRUE, connects to GEO FTP server via HTTPS (https://ftp.ncbi.nlm.nih.gov/geo); otherwise uses plain FTP (ftp://ftp.ncbi.nlm.nih.gov/geo). Only applicable to GEO FTP server access.

handle_opts

A list of named options / headers to be set in the multi_download.

odir

Destination directory for downloads. Defaults to the current working directory.

Value

A GEOSoft object

Details

The Gene Expression Omnibus (GEO) from NCBI serves as a public repository for a wide range of high-throughput experimental data. These data include single and dual channel microarray-based experiments measuring mRNA, genomic DNA, and protein abundance, as well as non-array techniques such as serial analysis of gene expression (SAGE), and mass spectrometry proteomic data. At the most basic level of organization of GEO, there are three entity types that may be supplied by users: Platforms, Samples, and Series. Additionally, there is a curated entity called a GEO dataset.

A Platform record describes the list of elements on the array (e.g., cDNAs, oligonucleotide probesets, ORFs, antibodies) or the list of elements that may be detected and quantified in that experiment (e.g., SAGE tags, peptides). Each Platform record is assigned a unique and stable GEO accession number (GPLxxx). A Platform may reference many Samples/Series that have been submitted by multiple submitters.

A Sample record describes the conditions under which an individual Sample was handled, the manipulations it underwent, and the abundance measurement of each element derived from it. Each Sample record is assigned a unique and stable GEO accession number (GSMxxx). A Sample entity must reference only one Platform and may be included in multiple Series.

A Series record defines a set of related Samples considered to be part of a group, how the Samples are related, and if and how they are ordered. A Series provides a focal point and description of the experiment as a whole. Series records may also contain tables describing extracted data, summary conclusions, or analyses. Each Series record is assigned a unique and stable GEO accession number (GSExxx).

GEO DataSets (GDSxxx) are curated sets of GEO Sample data. A GDS record represents a collection of biologically and statistically comparable GEO Samples and forms the basis of GEO's suite of data display and analysis tools. Samples within a GDS refer to the same Platform, that is, they share a common set of probe elements. Value measurements for each Sample within a GDS are assumed to be calculated in an equivalent manner, that is, considerations such as background processing and normalization are consistent across the dataset. Information reflecting experimental design is provided through GDS subsets.

Examples

# \donttest{
gse <- geo_soft("GSE10", odir = tempdir())
#> Found 1 file already downloaded
gpl <- geo_soft("gpl98", odir = tempdir())
#> Downloading 1 file
gsm <- geo_soft("GSM1", odir = tempdir())
#> Downloading 1 file
gds <- geo_soft("GDS10", odir = tempdir())
#> Downloading 1 file
# }