doFishersEnrichmentForGeneNames: Perform a gene set enrichment using gene list based on common...

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

Description

Perform an enrichment of an input gene list using the Atlas as a background set for a specified species. The genes are given as a set of common gene names (e.g. Brca1). The results are a list of experimental factors for which these genes are enriched. Access the backgroun data sets for enrichment from https://github.com/jamesmalone/AtlasRDF-R

Usage

    doFishersEnrichmentForGeneNames(genenames, taxon, genelist_bg, genecounts, endpoint="http://www.ebi.ac.uk/rdf/services/atlas/sparql")

Arguments

genenames	Variable genenames a vector of genes using common gene names
taxon	The taxon is an ontology URI which can be found using the function getTaxonURI()
genelist_bg	genelist_bg background list appropriate for the species of interest should be obtained from svn
genecounts	genecounts counts list appropriate for the species of interest should be obtained from svn
endpoint	SPARQL endpoint to query data from. Default value is the live Atlas SPARQL endpoint but this can be overidden. Required to find Gene URIs from gene names

Value

Returns a list of enrichmentresult objects which are described as follows:

factoruri	the URI of the experimental factor
label	the human readable label for the experimental factor
p.value	the p.value for the Fisher's exact test for the gene list with this factor. This can be seen as avidence for this factor being highly enriched (low p value) or not (high p value) for the input gene list
estimate	an estimate of the odds ratio. Note that the conditional Maximum Likelihood Estimate (MLE) rather than the unconditional MLE (the sample odds ratio) is used. Only present in the 2 by 2 case.
alternative	a character string describing the alternative hypothesis.
null.value	the odds ratio under the null, or. Only present in the 2 by 2 case.
method	the character string "Fisher's Exact Test for Count Data".
enrichedgenes	list of the genes from the input gene list that were enriched for this factor as a list of Gene URIs. To get the gene names use the function getClassLabel

Author(s)

James Malone, European Bioinformatics Institute Simon Jupp, European Bioinformatics Institute Maryam Soleimani, European Bioinformatics Institute

References

Agresti, A. (1990) Categorical data analysis. New York: Wiley. Pages 59-66.

Examples

    
    ###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)
    #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)
    
   

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