DAVIDResult-class: class "DAVIDResult
Description
This class represents the most generic result obtained in
the Database for Annotation,
Visualization and Integrated
Discovery (DAVID) website (see References).
Type
This class is a "Virtual" one.Heirs
-
DAVIDGenes: basic gene information
(ID, Name and Specie)
-
DAVIDCluster: generic
Cluster result (Term or Gene).
-
DAVIDFunctionalAnnotationChart: EASE results on
each Functional Category (see references).
-
DAVIDFunctionalAnnotationTable: annotation for
each gene, no statistical analysis.
Slots
type- Object of class
"character". Contains the name of DAVID's result.
Methods
showsignature(object="DAVIDResult"):
returns a basic console output.typesignature(object="DAVIDResult"):
getter for type slot.plot2Dsignature(object="DAVIDResult",
dataFrame="data.frame"): internal ggplot tile plot for
gene/term cluster and annotation heirs.
References
- The Database for Annotation,
Visualization and Integrated Discovery
(david.abcc.ncifcrf.gov)
- 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
- Huang, D. W.; Sherman, B.
T. & Lempicki, R. A. Bioinformatics enrichment tools:
paths toward the comprehensive functional analysis of
large gene lists. Nucleic Acids Res, Laboratory of
Immunopathogenesis and Bioinformatics, Clinical Services
Program, SAIC-Frederick, Inc., National Cancer Institute
at Frederick, Frede#rick, MD 21702, USA., 2009, 37, 1-13
- Xiaoli Jiao, Brad T. Sherman, Da Wei Huang, Robert
Stephens, Michael W. Baseler, H. Clifford Lane, Richard
A. Lempicki, DAVID-WS: A Stateful Web Service to
Facilitate Gene/Protein List Analysis Bioinformatics 2012
doi:10.1093/bioinformatics/bts251