AtlasRDF-package: Gene Expression Atlas query and gene set enrichment package.

In AtlasRDF: Gene Expression Atlas query and gene set enrichment package.

Description

Query the Gene Expression Atlas RDF data at the European Bioinformatics Institute using genes, experimental factors (such as disease, cell type, compound treatments), pathways and proteins. Also contains a function to perform an enrichment of your gene list across Experimental Factor Ontology (EFO) using the Atlas background set. Access the backgroun data sets for enrichment from https://github.com/jamesmalone/AtlasRDF-R

Details

Package:	AtlasRDF
Type:	Package
Version:	1.3
Date:	2015-01-26
License:	Apache 2.0

Note

Linux users may need to perform the following:

sudo apt-get install libxml2-dev

from R environment: install.package("XML")

sudo apt-get install libcurl4-gnutls-dev

from R environment: install.package("RCurl")

from R environment: install.package("hash")

from R environment: install.package("SPARQL")

Author(s)

James Malone, Simon Jupp, Maryam Soleimani

Maintainer: James Malone <[e-mail]>

References

Gene Expression Atlas RDF - http://wwwdev.ebi.ac.uk/rdf/services/atlas/ Gene Expression Atlas - http://www.ebi.ac.uk/gxa Experimental Factor Ontology - http://www.ebi.ac.uk/efo Kapushesky M, Adamusiak T, Burdett T, Culhane A, Farne A, Filippov A, Holloway E, Klebanov A, Kryvych N, Kurbatova N, Kurnosov P, Malone J, Melnichuk O, Petryszak R, Pultsin N, Rustici G, Tikhonov A, Travillian RS, Williams E, Zorin A, Parkinson H, Brazma A. (2012) Gene Expression Atlas update–a value-added database of microarray and sequencing-based functional genomics experiments. Nucleic Acids Res. 2012 Jan;40(Database issue):D1077-81.

Examples

    ###find experiments where the description contains a given search term
    #experimentlist <- getExperimentsByDescription("breast carcinoma")
    
    ###get gene list for given experiment ID
    #genelist <- getGenesForExperimentID("E-MEXP-3739")
    
    ###get list of pathways associated with a gene for which the genes are differentially expressed for a given condition (Type I diabetes in this case)
    pathwayinfo <- getPathwaysFromGenesAndCondition("efo:EFO_0001359")
    pathwayinfo$pathwayname
    
    ###perform gene set enrichment using Atlas as background to find factors genes are enriched for
    #load the background files for the species of interest (requires downloading)
    #find background sets at https://github.com/jamesmalone/AtlasRDF-R
    #load("human_gene_list.RData")   #human_genelist_bg
    #load("human_factor_counts.RData")    #human_factor_counts
    
    ###creat or load your genelist of interest
    genelist <- c("GSTT1", "PLCE1", "XIST", "ENOSF-1", "AHR", "FSTL1", "YIPF5", "RBM5", "TNP01", "CREB1", "NOX4", "FLII")
    
    ###get id for species 'human'
    taxon <-getTaxonURI("human")  #obo:NCBITaxon_9606
    
    ###do enrichment
    #results <- doFishersEnrichmentForGeneNames(genelist, taxon, human_genelist_bg, human_factor_counts)
    
    ###visualize results, filtering by p-value
    #vizPvalues(results, "0.005")

Example output

Loading required package: hash
hash-3.0.1 provided by Decision Patterns

Loading required package: SPARQL
Loading required package: XML
Loading required package: RCurl
Loading required package: bitops
An error occured when trying getPathwaysFromGenesAndCondition query Error in function (type, msg, asError = TRUE) : Could not resolve host: www.ebi.ac.uk

NULL
human

AtlasRDF documentation built on Nov. 17, 2017, 9:33 a.m.