# An R Package for retrieving data from DAVID into R objects using Web Services API.

## Documentation for package ‘RDAVIDWebService’ version 1.0.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

A B C D E F G I L M P S T U

DAVIDWebService-package | An R Package for retrieving data from DAVID into R objects using Web Services

## -- A --

addList | Methods to manipulate DAVID website
addList-method | Methods to manipulate DAVID website
annotationSummary1 | DAVID's website annotation summary example files
annotationSummary2 | DAVID's website annotation summary example files
annotationTable1 | DAVID's website functional annotation table example files
annotationTable2 | DAVID's website functional annotation table example files
as | High level constructors for DAVIDWebService package's classes.

## -- B --

benjaminis | Methods for 'DAVIDGODag' class object
benjaminis-method | Methods for 'DAVIDGODag' class object
bonferronis | Methods for 'DAVIDGODag' class object
bonferronis-method | Methods for 'DAVIDGODag' class object

## -- C --

categories | 'categories' for the different DAVIDWebService package class objects
categories-method | 'categories' for the different DAVIDWebService package class objects
cluster | Methods for 'DAVIDCluster' class object
cluster-method | Methods for 'DAVIDCluster' class object
cluster-methods | Methods for 'DAVIDCluster' class object
connect | Methods to manipulate DAVID website
connect-method | Methods to manipulate DAVID website
counts | Methods for 'DAVIDGODag' class object
counts-method | Methods for 'DAVIDGODag' class object

## -- D --

DAVIDCluster-class | class "DAVIDCluster
DAVIDFunctionalAnnotationChart | High level constructors for DAVIDWebService package's classes.
DAVIDFunctionalAnnotationChart-class | class "DAVIDFunctionalAnnotationChart
DAVIDFunctionalAnnotationChart-method | High level constructors for DAVIDWebService package's classes.
DAVIDFunctionalAnnotationChart-methods | High level constructors for DAVIDWebService package's classes.
DAVIDFunctionalAnnotationTable | High level constructors for DAVIDWebService package's classes.
DAVIDFunctionalAnnotationTable-class | class "DAVIDFunctionalAnnotationTable
DAVIDFunctionalAnnotationTable-method | High level constructors for DAVIDWebService package's classes.
DAVIDFunctionalAnnotationTable-methods | High level constructors for DAVIDWebService package's classes.
DAVIDGeneCluster | High level constructors for DAVIDWebService package's classes.
DAVIDGeneCluster-class | class "DAVIDGeneCluster
DAVIDGeneCluster-method | High level constructors for DAVIDWebService package's classes.
DAVIDGeneCluster-methods | High level constructors for DAVIDWebService package's classes.
DAVIDGenes | High level constructors for DAVIDWebService package's classes.
DAVIDGenes-class | class "DAVIDGenes
DAVIDGenes-method | High level constructors for DAVIDWebService package's classes.
DAVIDGenes-methods | High level constructors for DAVIDWebService package's classes.
DAVIDGODag | High level constructors for DAVIDWebService package's classes.
DAVIDGODag-class | class "DAVIDGODag
DAVIDGODag-method | High level constructors for DAVIDWebService package's classes.
DAVIDGODag-methods | High level constructors for DAVIDWebService package's classes.
DAVIDResult-class | class "DAVIDResult
DAVIDTermCluster | High level constructors for DAVIDWebService package's classes.
DAVIDTermCluster-class | class "DAVIDTermCluster
DAVIDTermCluster-method | High level constructors for DAVIDWebService package's classes.
DAVIDTermCluster-methods | High level constructors for DAVIDWebService package's classes.
DAVIDWebService | Main class to connect to DAVID Web Service
DAVIDWebService-class | Main class to connect to DAVID Web Service
demoList1 | DAVID's website demoList1 example id files
demoList2 | DAVID's website demoList1 example id files
dictionary | Methods for 'DAVIDFunctionalAnnotationTable' class object
dictionary-method | Methods for 'DAVIDFunctionalAnnotationTable' class object
dictionary-methods | Methods for 'DAVIDFunctionalAnnotationTable' class object
duplicateIds | Methods for 'DAVIDGenes' class object
duplicateIds-method | Methods for 'DAVIDGenes' class object
duplicateIds-methods | Methods for 'DAVIDGenes' class object

## -- E --

enrichment | Methods for 'DAVIDCluster' class object
enrichment-method | Methods for 'DAVIDCluster' class object

## -- F --

fdrs | Methods for 'DAVIDGODag' class object
fdrs-method | Methods for 'DAVIDGODag' class object
foldEnrichments | Methods for 'DAVIDGODag' class object
foldEnrichments-method | Methods for 'DAVIDGODag' class object
funChart1 | DAVID's website Functional Annotation Chart example files
funChart2 | DAVID's website Functional Annotation Chart example files

## -- G --

geneCluster1 | DAVID's website gene/term cluster report example files
geneCluster2 | DAVID's website gene/term cluster report example files
geneList1 | DAVID's website gene list example files
geneList2 | DAVID's website gene list example files
genes | 'genes' for the different DAVIDWebService package class objects.
genes-method | 'genes' for the different DAVIDWebService package class objects.
genes-methods | 'genes' for the different DAVIDWebService package class objects.
getAllAnnotationCategoryNames | Methods to manipulate DAVID website
getAllAnnotationCategoryNames-method | Methods to manipulate DAVID website
getAnnotationSummary | Obtain DAVID website reports
getAnnotationSummary-method | Obtain DAVID website reports
getBackgroundListNames | Methods to manipulate DAVID website
getBackgroundListNames-method | Methods to manipulate DAVID website
getClusterReport | Obtain DAVID website reports
getClusterReport-method | Obtain DAVID website reports
getClusterReportFile | Obtain DAVID website reports
getClusterReportFile-method | Obtain DAVID website reports
getCurrentBackgroundListPosition | Methods to manipulate DAVID website
getCurrentBackgroundListPosition-method | Methods to manipulate DAVID website
getCurrentGeneListPosition | Methods to manipulate DAVID website
getCurrentGeneListPosition-method | Methods to manipulate DAVID website
getCurrentSpeciesPosition | Methods to manipulate DAVID website
getCurrentSpeciesPosition-method | Methods to manipulate DAVID website
getDefaultCategoryNames | Methods to manipulate DAVID website
getDefaultCategoryNames-method | Methods to manipulate DAVID website
getEmail | Accessor methods for 'DAVIDWebService' class
getEmail-method | Accessor methods for 'DAVIDWebService' class
getFunctionalAnnotationChart | Obtain DAVID website reports
getFunctionalAnnotationChart-method | Obtain DAVID website reports
getFunctionalAnnotationChartFile | Obtain DAVID website reports
getFunctionalAnnotationChartFile-method | Obtain DAVID website reports
getFunctionalAnnotationTable | Obtain DAVID website reports
getFunctionalAnnotationTable-method | Obtain DAVID website reports
getFunctionalAnnotationTableFile | Obtain DAVID website reports
getFunctionalAnnotationTableFile-method | Obtain DAVID website reports
getGeneCategoriesReport | Obtain DAVID website reports
getGeneCategoriesReport-method | Obtain DAVID website reports
getGeneListNames | Methods to manipulate DAVID website
getGeneListNames-method | Methods to manipulate DAVID website
getGeneListReport | Obtain DAVID website reports
getGeneListReport-method | Obtain DAVID website reports
getGeneListReportFile | Obtain DAVID website reports
getGeneListReportFile-method | Obtain DAVID website reports
getIdTypes | Methods to manipulate DAVID website
getIdTypes-method | Methods to manipulate DAVID website
getListName | Methods to manipulate DAVID website
getListName-method | Methods to manipulate DAVID website
getSpecieNames | Methods to manipulate DAVID website
getSpecieNames-method | Methods to manipulate DAVID website
getStub | Accessor methods for 'DAVIDWebService' class
getStub-method | Accessor methods for 'DAVIDWebService' class

## -- I --

ids | 'ids' for the different DAVIDWebService package class objects
ids-method | 'ids' for the different DAVIDWebService package class objects
initialize | High level constructors for DAVIDWebService package's classes.
initialize-method | High level constructors for DAVIDWebService package's classes.
is.connected | Methods to manipulate DAVID website
is.connected-method | Methods to manipulate DAVID website

## -- L --

listTotals | Methods for 'DAVIDGODag' class object
listTotals-method | Methods for 'DAVIDGODag' class object

## -- M --

members | Methods for 'DAVIDCluster' class object
members-method | Methods for 'DAVIDCluster' class object
membership | Methods for 'DAVIDFunctionalAnnotationTable' class object
membership-method | Methods for 'DAVIDFunctionalAnnotationTable' class object
membership-methods | Methods for 'DAVIDFunctionalAnnotationTable' class object

## -- P --

percentages | Methods for 'DAVIDGODag' class object
percentages-method | Methods for 'DAVIDGODag' class object
plot2D | Visualization of biological relationships
plot2D-method | Visualization of biological relationships
plot2D-methods | Visualization of biological relationships
popHits | Methods for 'DAVIDGODag' class object
popHits-method | Methods for 'DAVIDGODag' class object
popTotals | Methods for 'DAVIDGODag' class object
popTotals-method | Methods for 'DAVIDGODag' class object

## -- S --

setAnnotationCategories | Methods to manipulate DAVID website
setAnnotationCategories-method | Methods to manipulate DAVID website
setCurrentBackgroundPosition | Methods to manipulate DAVID website
setCurrentBackgroundPosition(position) | Methods to manipulate DAVID website
setCurrentBackgroundPosition-method | Methods to manipulate DAVID website
setCurrentGeneListPosition | Methods to manipulate DAVID website
setCurrentGeneListPosition-method | Methods to manipulate DAVID website
setCurrentSpecies | Methods to manipulate DAVID website
setCurrentSpecies-method | Methods to manipulate DAVID website
setEmail | Accessor methods for 'DAVIDWebService' class
setEmail-method | Accessor methods for 'DAVIDWebService' class
show | Basic console output
show-method | Basic console output
species | Methods for 'DAVIDGenes' class object
species-method | Methods for 'DAVIDGenes' class object
species-methods | Methods for 'DAVIDGenes' class object
subset | Methods for 'DAVIDFunctionalAnnotationTable' class object
subset-method | Methods for 'DAVIDFunctionalAnnotationTable' class object
summary | Basic summary for DAVIDWebService package classes.
summary-method | Basic summary for DAVIDWebService package classes.

## -- T --

termCluster1 | DAVID's website gene/term cluster report example files
termCluster2 | DAVID's website gene/term cluster report example files
terms | Methods for 'DAVIDGODag' class object
terms-method | Methods for 'DAVIDGODag' class object
type | Getters for 'DAVIDResult' object
type-method | Getters for 'DAVIDResult' object

## -- U --

uniqueIds | Methods for 'DAVIDGenes' class object
uniqueIds-method | Methods for 'DAVIDGenes' class object
universeCounts | Methods for 'DAVIDGODag' class object
universeCounts-method | Methods for 'DAVIDGODag' class object
universeMappedCount | Methods for 'DAVIDGODag' class object
universeMappedCount-method | Methods for 'DAVIDGODag' class object
upsideDown | Methods for 'DAVIDGODag' class object
upsideDown-method | Methods for 'DAVIDGODag' class object