GEO URL resolver

Construct and resolve URLs for GEO (Gene Expression Omnibus) resources. This function provides a unified interface for accessing GEO data either via Accession Display Bar of GEO database or directly from GEO FTP/HTTPS servers. Depending on the accession type or requested format and amount, it automatically generates the correct URL.

Usage

geo_url(
  accession,
  format = NULL,
  amount = NULL,
  scope = NULL,
  ftp_over_https = NULL
)

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.

format

A character specifying file format type requested. GEO data can be accessed through two sites:

• Direct FTP/HTTPS file retrieval from GEO FTP server (file type):

  • "soft": SOFT (Simple Omnibus in Text Format) from GEO FTP site. When accession is DataSets or Series, this is the default.

  • "soft_full": full SOFT (Simple Omnibus in Text Format) files from GEO FTP site by DataSet (GDS) containging additionally contains up-to-date gene annotation for the DataSet Platform.

  • "miniml": MINiML (MIAME Notation in Markup Language, pronounced miniml) is an XML format that incorporates experimental data and metadata. MINiML is essentially an XML rendering of SOFT format.

  • "matrix": Series matrix file.

  • "annot": annotation files for Platforms.

  • "suppl": supplementary files.

• For file retrieval from Accession Display Bar of GEO database:

  • "text": machine-readable SOFT format (Simple Omnibus Format in Text).

  • "xml": XML format.

  • "html": human-readable format with hyperlinks (no downloadable entry available).

  The following table summarizes the compatibility between GEO accession types and file format options:

  format	GDS	GSE	GPL	GSM
  SOFT (soft)	o	o	o	x
  SOFTFULL (soft_full)	o	x	x	x
  MINiML (miniml)	x	o	o	x
  Matrix (matrix)	x	o	x	x
  Annotation (annot)	x	x	o	x
  Supplementaryfiles (suppl)	x	o	o	o
  Html (html)	o	o	o	o
  Text (text)	x	o	o	o
  Xml (xml)	x	o	o	o

amount

A character specifying the amount of data (Only applicable to Accession Display Bar access):

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

• "brief": accession attributes only.

• "quick": accession attributes + first 20 rows of the data table.

• "data": omits the accession's attributes, showing only links to other accessions and the full data table.

• "full": accession attributes + complete data table.

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.

Value

A character of GEO URL.

References

• https://www.ncbi.nlm.nih.gov/geo/info/download.html

• https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi

• https://www.ncbi.nlm.nih.gov/geo/info/soft.html#format

• Programmatic access to GEO FTP site

Examples

geo_url("GSE10")
#> [1] "https://ftp.ncbi.nlm.nih.gov/geo/series/GSEnnn/GSE10/soft/GSE10_family.soft.gz"
geo_url("gpl98")
#> [1] "https://ftp.ncbi.nlm.nih.gov/geo/platforms/GPLnnn/GPL98/soft/GPL98_family.soft.gz"
geo_url("GSM1")
#> [1] "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1&targ=self&view=data&form=text"
geo_url("GDS10")
#> [1] "https://ftp.ncbi.nlm.nih.gov/geo/datasets/GDSnnn/GDS10/soft/GDS10.soft.gz"