DAVIDGenes-class {RDAVIDWebService} | R Documentation |
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.
This class is a "Concrete
" one.
DAVIDResult
in the conceptual way.
data.frame
in order to extend the basic
features.
none additional to the ones inherited from DAVIDResult and data.frame classes.
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.
Cristobal Fresno and Elmer A Fernandez
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
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
{ ##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) }