class "DAVIDGenes

Description

This class represents the output of "Show Genes Result" of DAVID. It is an heir of DAVIDResult in the conceptual way, and also a data.frame with additional features, such as identifying the unique and duplicate ids, searching for genes with a given id, etc.

Type

This class is a "Concrete" one.

Extends

• DAVIDResult in the conceptual way.

• data.frame in order to extend the basic features.

Slots

none additional to the ones inherited from DAVIDResult and data.frame classes.

Methods

valid

signature(object="DAVIDGenes"): logical which checks for data.frame name (ID, Name) presence.

DAVIDGenes

signature(object="character"): constructor with the name of the .tab file report to load.

DAVIDGenes

signature(object="data.frame"): data.frame already loaded to use when constructing the object.

ids

signature(object="DAVIDGenes"): character vector with gene submitted ids.

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 DAVIDGenes: DAVIDFunctionalAnnotationChart, DAVIDFunctionalAnnotationChart, DAVIDFunctionalAnnotationChart, DAVIDFunctionalAnnotationTable, DAVIDFunctionalAnnotationTable, DAVIDFunctionalAnnotationTable, DAVIDGODag, DAVIDGODag, DAVIDGeneCluster, DAVIDGeneCluster, DAVIDGenes, DAVIDGenes, DAVIDGenes, DAVIDTermCluster, DAVIDTermCluster, as, as, as, genes, genes, genes, genes, ids, ids, ids, ids, ids, initialize, initialize, initialize, initialize, initialize, initialize, initialize

Examples

{
##Load Show Gene List file report for the input demo file 1, using data
##function. Then, create a DAVIDGenes object using the loaded data.frame
##geneList1. In addition, the user can use the file name of the downloaded
##file report.
data(geneList1)
davidGenes1<-DAVIDGenes(geneList1)

##Now we can inspect davidGenes1 as it was an common data.frame
head(davidGenes1)

##Additional getters for this object are also available, to obtain the
##different columns: ids, genes and species.
ids(davidGenes1)
genes(davidGenes1)
species(davidGenes1)

##Or even look up for a particular gene id, which will return only the
##matched ones.
genes(davidGenes1, ids=c("38926_at", "35367_at", "no match"))

##Obtain the genes with duplicate manufacturer ids or just the genes that
##do not have duplicate ids (uniqueIds).
duplicateIds(davidGenes1)
uniqueIds(davidGenes1)
}