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Accessors for GEOquery objects

Source: R/GEOquery-package.R
GEOData-accessors.Rd

Accessor generics for the S4 objects returned by getGEO when parsing SOFT-format records (GSE, GSM, GPL, GDS). Use these rather than reaching into slots directly.

Arguments

object

A GEOquery S4 object (GSE, GSM, GPL, GDS, or GEODataTable).

Value

Meta() a list; Accession() a character string; Table() and Columns() data.frames; dataTable() a GEODataTable; GSMList() and GPLList() named lists.

Details

Meta(object)

The record metadata as a named list (title, submission dates, sample/platform attributes, and so on).

Accession(object)

The GEO accession (the geo_accession metadata field).

Table(object)

The data table as a data.frame – for example the measurement table of a GSM or the probe annotation of a GPL.

Columns(object)

A data.frame describing the columns of Table(object).

dataTable(object)

The underlying GEODataTable object, which holds both Table() and Columns().

GSMList(object)

For a GSE, the list of its GSM sample objects.

GPLList(object)

For a GSE, the list of its GPL platform objects.

See also

GEOData-class, getGEO

Author

Sean Davis

Examples

if (FALSE) { # \dontrun{
  gsm <- getGEO("GSM11805")
  Meta(gsm)$title
  head(Table(gsm))
  Columns(gsm)

  gse <- getGEO("GSE781", GSEMatrix = FALSE)
  names(GSMList(gse))
} # }