get_geo: Get a GEO object from GEO FTP site
In Yunuuuu/rgeo: R interface for GEO database

View source: R/get_geo.R

get_geo

R Documentation

Get a GEO object from GEO FTP site

Description

This function is the main user-level function in the rgeo package. It implements the downloading and parsing of GEO files.

Usage

get_geo(
  ids,
  dest_dir = getwd(),
  gse_matrix = TRUE,
  pdata_from_soft = TRUE,
  add_gpl = NULL,
  ftp_over_https = TRUE,
  handle_opts = list(connecttimeout = 60L)
)

Arguments

`ids`	A character vector representing the GEO entity for downloading and parsing. All ids must in the same GEO identity (`c("GDS505", "GDS606")` are all GEO DataSets, `c("GSE2", "GSE22")` are all GEO series eg.).
`dest_dir`	The destination directory for any downloads. Defaults to current working dir.
`gse_matrix`	A logical value indicates whether to retrieve Series Matrix files when handling a `GSE` GEO entity. When set to `TRUE`, an ExpressionSet Object will be returned.
`pdata_from_soft`	A logical value indicates whether derive `phenoData` from GSE series soft file when parsing ExpressionSet Object. Defaults to `TRUE`. Sometimes soft file can be in large size, you can disable the downloading of soft file by setting pdata_from_soft into `FALSE`. if `FALSE`, `phenoData` will be parsed directly from GEO series matrix file, which is what `GEOquery` do, in this way, `⁠characteristics_ch*⁠` column sometimes cannot be parsed correctly.
`add_gpl`	A logical value indicates whether to add platform (namely the featureData slot in the ExpressionSet Object) information when handling a `GSE` GEO entity with `gse_matrix` option `TRUE`. `add_gpl` is set to `NULL` by default, which means the internal will try to map the GPL accession ID into a Bioconductor annotation package firstly, if it succeed, the annotation slot in the returned ExpressionSet object will be set to the found Bioconductor annotation package and the `add_gpl` will be set to `FALSE`, otherwise, `add_gpl` will be set to `TRUE`.
`ftp_over_https`	A scalar logical value indicates whether to connect GEO FTP site with https traffic. If `TRUE`, will download FTP files from https://ftp.ncbi.nlm.nih.gov/geo, which is used by GEOquery, otherwise, will use ftp://ftp.ncbi.nlm.nih.gov/geo directly.
`handle_opts`	A list of named options / headers to be set in the handle.

Details

Use get_geo functions to download and parse information available from NCBI GEO. Here are some details about what is avaible from GEO. All entity types are handled by get_geo and essentially any information in the GEO SOFT format is reflected in the resulting data structure.

From the GEO website:

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 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.

Value

An object of the appropriate class (GDS, GPL, GSM, or GSE) is returned. For GSE entity, if gse_matrix parameter is FALSE, an GEOSeries object is returned and if gse_matrix parameter is TRUE, a ExpressionSet Object or a list of ExpressionSet Objects is returned with every element correspongding to each Series Matrix file associated with the GSE accesion. And for other GEO entity, a GEOSoft object is returned.

References

Examples

gse_matix <- get_geo("GSE10", tempdir())
gse <- get_geo("GSE10", tempdir(), gse_matrix = FALSE)
gpl <- get_geo("gpl98", tempdir())
gsm <- get_geo("GSM1", tempdir())
gds <- get_geo("GDS10", tempdir())

Yunuuuu/rgeo documentation built on Dec. 23, 2024, 10:01 p.m.