gwasGOenrich: Calculate Enrichment of GO Terms in GWAS Datasets

Description Usage Arguments Details Value References

View source: R/gwasGOenrich.R

Description

This function wraps functionality from the topGO package, providing a simplified interface for GO term enrichment for GWAS datasets. Before running this function on a GWAS dataset, a SNP to gene mapping and calculation of gene-wise p-values has to be applied to the GWAS dataset, e.g. as offered by the snp2gene and gene2p functions.

Usage

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gwasGOenrich(
    gwas, 
    ontology = "BP", 
    pkgname.GO = "org.Hs.eg.db", 
    topGOalgorithm = "weight01",
    pruneTermsBySize = 10, 
    plotSigTermsToFile = 5
)

Arguments

gwas

data frame. Has to contain a column of gene-wise p-values (see also gene2p named 'gene.p' and a column named 'geneid' or 'genename' containing entrez IDs, ensembl gene IDs, gene symbols or names, respectively.

ontology

character(1). Can be "BP", "MF" or "CC" to use the according ontology for enrichment (i.e. biological process, molecular function, cellular component).

pkgname.GO

character(1). Name of the GO annotation package to use. This is 'org.Hs.eg.db' for human datasets, but alternative 'org...' packages which are available via bioconductor for different organisms can be specified.

topGOalgorithm

character(1). Is passed to the algorithm argument of topGO. Possible values are listed by running whichAlgorithms. E.g. 'elim' decorrelates the GO tree so that the most specific out of several similar terms is contained in the results, and 'weight01' has a similar effect. The 'classic' option will just run the test on all terms.

pruneTermsBySize

numeric(1). Is passed to the nodeSize argument of topGO. When >1, all GO terms with less than pruneTermsBySize genes will be discarded before the enrichment.

plotSigTermsToFile

numeric(1). When > 0, the topGO method printGraph will be called to produce a file containing a graph plot of the most significant terms and its descendant terms, together with enrichment stats. The storeGraphPlot most significant terms will be contained in the plot.

Details

This function builds a topGO data object at hand of the supplied gwas dataset and applies runTest with the statistic = "ks" option which runs a gene-set enrichment like analyis.

Value

A data frame with columns 'go_id', 'Term' and 'P' containing identifier, description and enrichment p-value of all GO terms tested. When plotSigTerms is > 0, a pdf file (name starting with 'enrichment...) will be produced as a side effect containing the graph plot for selected terms produced by topGO.

References

Adrian Alexa and Jorg Rahnenfuhrer (2010). topGO: topGO: Enrichment analysis for Gene Ontology. R package version 2.8.0.


merns/postgwas documentation built on May 22, 2017, 4:16 a.m.