GOFunction (version 1.20.0)

globalRedundancy: Treating for glocal redundancy between GO terms which share multiple function genes but have no ancient-offspring relationship

Description

For a pair of terms with overlapping genes, this function can identify whether their significance might be simply introduced by the overlapping genes (see details).

Arguments

generalAnn

generalAnn is the mapping between gene and GO terms.

sigTermRelation

sigTermRelation is the GO DAG relationship between the statistically significant terms.

annRef

annRef is the annotated reference genes and their annotated terms.

annInterest

annInterest is the annotated interesting genes and their annotated terms.

sigTermRedun

sigTermRedun is the remained statistically signifcant terms after treating local redundancy.

poth

poth is the significant level to test whether the overlapping genes of one term is significantly different from the non-overlapping genes of the term. The default is 0.05.

peth

peth is the significant level to test whether the non-overlapping genes of one term is enriched with interesting genes. The default is 0.05.

Value

The function returns a set of remained terms with evidence that their significance should not be simply due to the overlapping genes.

Details

This function uses the following principles to treat for glocal redundancy between GO terms which share multiple function genes but have no ancient-offspring relationship. For a pair of overlapping terms, GO-function remains one term only if (1) there is additional evidence that the non-overlapping genes of a term may be related to the disease if the frequency of interesting genes in these genes is not significantly different from that in the overlapping genes or is significantly higher than the random background; and (2) there is no such evidence for the non-overlapping genes of another term. In all the other situations, GO-function remains both terms.

See Also

GOFunction localRedundancy