get_GOterm2GeneAssos: get GO-gene associations

In PengNi/dSimer: Integration of Disease Similarity Methods

Description

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

Usage

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

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

PengNi/dSimer documentation built on May 8, 2019, 1:28 a.m.