Calculate interaction based homogeneity for a gene list according to the BioGRID Interactions

Description

This function calculated interactios based homogeneity for a gene list according to the BioGRID Interactions for seven organisms: Arabidopsis thaliana(arabidopsis), Caenerhabditis elegans(c.elegans), Drosophila melanogaster (fruitFly), Homo sapiens (human), Mus musculus (mouse), Saccharomyces cerevisae (yeast), Schizosaccharomyces pombe (s.pombe). Unique ids(systematic names), official names or Entrez ids can be used as identifier type.

Usage

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ibhBioGRID(geneList, organism, idType = "EntrezId")

Arguments

geneList

list of genes/proteins for which interaction based homogeneity is evaluated

organism

Organism name. Can be one of 'arabidopsis', 'c.elegans', 'fruitFly', 'human', 'mouse', 'yeast', 's.pombe'.

idType

Type of identifier used. Can be one of 'EntrezId', 'Official' and 'UniqueId'

Value

Float representing interaction based homogeneity for each list

References

Stark C, Breitkreutz BJ, Reguly T, Boucher L, Breitkreutz A, Tyers M. Biogrid: A General Repository for Interaction Datasets. Nucleic Acids Res. Jan1; 34:D535-9

See Also

ibh,ibhForMultipleGeneListsBioGRID

Examples

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	require(simpIntLists)
	geneList <-  list(839226,817241, 824340, 832179, 818561, 831145, 838782, 826404);
	ibhBioGRID(geneList, organism="arabidopsis",
						idType = "EntrezId");
	geneList <- list("YJR151C", "YBL032W",   "YAL040C",   "YBL072C",   "YCL050C",   "YCR009C");
	ibhBioGRID(geneList, organism="yeast", idType = "UniqueId");