GOFunction (version 1.20.0)

localRedundancy: Treating for local redundancy between GO terms with ancient-offspring relationship

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.

Value

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

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.

See Also

GOFunction enrichmentFunction