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GEO URL resolver

Source: R/geo-.R
geo_url.Rd

Construct and resolve URLs for GEO (Gene Expression Omnibus) resources. This function provides a unified interface for accessing GEO data either via NCBI’s accession-based query system or directly from GEO FTP/HTTPS servers. Depending on the accession type or requested famount, it automatically generates the correct URL.

Usage

geo_url(
  accession,
  famount = NULL,
  format = NULL,
  scope = NULL,
  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.

famount

A character specifying file/amount 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.

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

    famountGDSGSEGPLGSM
    SOFT (soft)ooox
    SOFTFULL (soft_full)oxxx
    MINiML (miniml)xoox
    Matrix (matrix)xoxx
    Annotation (annot)xxox
    Supplementaryfiles (suppl)xooo

  • Accession-based queries to the NCBI GEO database (amount of data):

    • "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.

format

A character specifying the output format (Only applicable to NCBI GEO database access):

  • "none": Applicable only to DataSets; for DataSets, this is also the sole valid option (no downloadable entry available).

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

  • "xml": XML format.

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

scope

A character specifying which GEO accessions to include (Only applicable to NCBI GEO database 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).

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.