class "DAVIDCluster

Description

This virtual class represents the output of a DAVID "Cluster" report, with "DAVIDTermCluster" and "DAVIDGeneCluster" as possible heirs, according to the report used.

Type

This class is a "Virtual" one.

Extends

• DAVIDResult in the conceptual way.

Heirs

• DAVIDTermCluster: DAVID's Functional Annotation Clustering report.

• DAVIDGeneCluster: DAVID's Functional Classification Tool report.

Slots

cluster

named list with the different clustered terms/genes: Members, represented as DAVIDGenes object; and EnrichmentScore, a numeric with DAVID cluster enrichment score.

Methods

show

signature(object="DAVIDCluster"): basic console output.

summary

signature(object="DAVIDCluster"): basic summary console output.

initialize

signature(object="DAVIDCluster", fileName="character"): basic cluster report file parser.

cluster

signature(object="DAVIDCluster"): getter for the corresponding slot.

enrichment

signature(object="DAVIDCluster"): obtain the enrichment score of each cluster.

members

signature(object="DAVIDCluster"): obtain the corresponding cluster members.

Author(s)

Cristobal Fresno and Elmer A Fernandez

References

1. The Database for Annotation, Visualization and Integrated Discovery (david.abcc.ncifcrf.gov)

2. Huang, D. W.; Sherman, B. T.; Tan, Q.; Kir, J.; Liu, D.; Bryant, D.; Guo, Y.; Stephens, R.; Baseler, M. W.; Lane, H. C.; Lempicki, R. A. DAVID Bioinformatics Resources: expanded annotation database and novel algorithms to better extract biology from large gene lists. Nucleic Acids Res, Laboratory of Immunopathogenesis and Bioinformatics, SAIC-Frederick, Inc., National Cancer Institute at Frederick, MD 21702, USA., 2007, 35, W169-W175

See Also

Other DAVIDCluster: cluster, cluster, dictionary, dictionary, enrichment, enrichment, members, members, membership, membership, subset, subset, summary, summary, summary, summary

Results