gwasGOenrich: Calculate Enrichment of GO Terms in GWAS Datasets
In merns/postgwas: GWAS Post-Processing Utilities

Description Usage Arguments Details Value References

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.

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

`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.

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.

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.

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, 2019, 6:53 p.m.