localRedundancy: Treating for local redundancy between GO terms with...

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

Description

This function uses some explicit rules to treat local redundancy (see details).

Arguments

sigTerm	sigTerm is the statistically significant terms found by the enrichmentFunction function.
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.
ppth	ppth is the significant level to test whether the remaining genes of the ancestor term are enriched with interesting genes after removing the genes in its significant offspring terms. The default is 0.05.
pcth	pcth is the significant level to test whether the frequency of interesting genes in the offspring terms are significantly different from that in the ancestor term. The default is 0.05.

Details

This function uses three principles to treat local redundancy between GO terms with ancient-offspring relationship: 1. if the frequency of interesting genes in the remaining genes of the ancestor term is not significantly higher than the random background, and at the same time, it is lower than the frequency of its significant offspring terms, GO-function only remains the offspring terms; Otherwise, GO-function remains ancient term. In this situation, 2. if the offspring terms are no different with the ancient term, GO-function only remains the ancestor term; otherwise, 3. GO-function remains both ancient term and its offspring terms.

Value

The function returns a set of remained terms without local redundancy.

Author(s)

Jing Wang

See Also

GOFunction enrichmentFunction

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