globalRedundancy: Treating for glocal redundancy between GO terms which share...

In GOFunction: GO-function: deriving biologcially relevant functions from statistically significant functions

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.

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.

Value

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

Author(s)

Jing Wang

See Also

GOFunction localRedundancy

GOFunction documentation built on April 28, 2020, 6:55 p.m.