get_GOterm2GeneAssos: get GO-gene associations

Description Usage Arguments Value Author(s) References See Also Examples

View source: R/data_preprocess.R

Description

get GO-gene associations from GO.db and org.Hs.eg.db

Usage

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get_GOterm2GeneAssos(GOONTOLOGY = c("BP", "MF", "CC"),
  geneid = c("ENTREZID", "SYMBOL", "OMIM"), rm.IEAs = TRUE,
  rm.termlessthan3genes = TRUE)

Arguments

GOONTOLOGY

"BP" or "MF" or "CC

geneid

gene id type, "ENTREZID" or "SYMBOL"

rm.IEAs

logical value, remove GO terms with evidence "IEA" or not

rm.termlessthan3genes

logical value, remove terms whose number of annotated genes are less than 3 or not

Value

a list which names are GO term IDs and elements are gene ids or symbols annotated with GO terms

Author(s)

Peng Ni, Min Li

References

Mathur S, Dinakarpandian D. Finding disease similarity based on implicit semantic similarity[J]. Journal of biomedical informatics, 2012, 45(2): 363-371.

See Also

PSB, Sun_function

Examples

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go2g<-get_GOterm2GeneAssos(GOONTOLOGY="BP", geneid="SYMBOL")
go2g

dSimer documentation built on Nov. 17, 2017, 12:51 p.m.