GEO-class: Virtual class for holding GEO series, samples, platforms, and...

In Yunuuuu/rgeo: R interface for GEO database

Virtual class for holding GEO series, samples, platforms, and datasets.

Description

GEOData class, which contains two slots meta and accession, is the basic class (super class) of GEOSeries class and GEOSoft class. GEOSeries class contains extra two slots gsm and gpl special for GSE entity soft file and GEOSoft contains extra two slots columns and datatable special for GEO samples, platforms, and datasets.

Usage

## S4 method for signature 'GEOData'
show(object)

## S4 method for signature 'GEOData'
meta(object)

## S4 replacement method for signature 'GEOData'
meta(object) <- value

## S4 method for signature 'GEOData'
accession(object)

## S4 replacement method for signature 'GEOData'
accession(object) <- value

## S4 method for signature 'GEOSoft'
show(object)

## S4 method for signature 'GEOSoft'
columns(object)

## S4 replacement method for signature 'GEOSoft'
columns(object) <- value

## S4 method for signature 'GEOSoft'
datatable(object)

## S4 replacement method for signature 'GEOSoft'
datatable(object) <- value

## S4 method for signature 'GEOSeries'
show(object)

## S4 method for signature 'GEOSeries'
gsm(object)

## S4 replacement method for signature 'GEOSeries'
gsm(object) <- value

## S4 method for signature 'GEOSeries'
gpl(object)

## S4 replacement method for signature 'GEOSeries'
gpl(object) <- value

Arguments

object	A GEO Class Object.
value	A R object with the same class of corresponding slots.

Slots

meta:

a list, containing the header metadata informations.

accession:

a character giving the geo accession id of current GEO series, samples, platforms, and datasets.

columns:

A data.frame gives the datatable header descriptions. The rownmaes of this data.frame should be the same with the column names of slot datatable.

datatable:

A data.frame shows the data information.

gsm:

a list of GEOSoft object containg the samples information of current GEO series.

gpl:

a list of GEOSoft object containg the platforms information of current GEO series.

Examples

 gse <- rgeo::get_geo("GSE10", tempdir(), gse_matrix = FALSE)
 accession(gse)
 gpllist <- gpl(gse)
 meta(gpllist[[1L]])
 accession(gpllist[[1L]])
 columns(gpllist[[1L]])
 datatable(gpllist[[1L]])

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