searchAtlasExperiments: Search for Expression Atlas experiments

In ebi-gene-expression-group/bioconductor-ExpressionAtlas: Download datasets from EMBL-EBI Expression Atlas

Search for Expression Atlas experiments

Description

This function accepts a vector of sample properties, and optionally a species name, and then searches for matching Expression Atlas experiments.

Usage

    searchAtlasExperiments( properties, species = NULL )

Arguments

properties	Character vector of sample properties to search Atlas for. These can be biological characteristics, experimental treatments, etc.
species	Optional. The name of a species to limit results to. If not provided, search is performed across all species in Expression Atlas.

Value

A DataFrame containing the ArrayExpress/BioStudies accessions, the species, experiment types, and titles of Expression Atlas experiments matching the query.

Examples

    
    # Search for experiments on salt in oryza (rice)
    atlasRes <- searchAtlasExperiments( properties = "salt", species = "oryza"  )

    # Download data for first experiment found.
    if ( nrow( atlasRes ) == 1 ) {
        atlasData <- getAtlasData( atlasRes$Accession )
    } else {
        atlasData <- getAtlasData( atlasRes$Accession[1] )
    }

ebi-gene-expression-group/bioconductor-ExpressionAtlas documentation built on Nov. 5, 2022, 4:21 a.m.