DAVIDWebService-class {RDAVIDWebService} | R Documentation

## Main class to connect to DAVID Web Service

### Description

A reference class to manage DAVID's Web Service connectivity, to run Set Enrichment Analysis (SEA) or Modular Enrichment Analysis (MEA) on a candidate list of gene/protein(s) with respect to a background list (the genome of the organism by default).

### Usage

      DAVIDWebService(...)

### Arguments

`...` | additional parameters. See Methods section.

### Details

`DAVIDWebService` class is implemented as a reference class, to manage a single instance connection to DAVIS's server by means of web services using a registered e-mail. For user registration, go to http://david.abcc.ncifcrf.gov/webservice/register.html. The implementation uses Java Remote Method Implementation (RMI) to connect the client and server side of DAVID. The main functionalities include:

1. Connectivity: upload gene/background list/s, change gene/background position, select current specie/s, select annotations, etc. from R.

2. Reports: Submitted Gene List, Annotation Category Summary, Gene/Term Clusters, Functional Annotation Chart and Functional Annotation Table as native R objects.

### Fields

`stub`:

  Java jobjRef which corresponds to a sample/session/client/stub/DAVIDWebServiceStub object for the client side of DAVID.

`email`:

  character.

### Methods

`show()`:

  prints DAVIDWebService object.

`summary()`:

  return a data.frame with a summary of all available annotations in DAVID in terms of percentage of gene list ids present in the category and numbers of terms where they can be found (see getAnnotationSummary)

`initialize(email="", ..., url)`:

  constructor for DAVIDWebService object, which includes: Java Virtual Machine initialization (... if required), and stub initialization with the provided email (if present) and using the url parameter for the API website.

`setEmail(mail)`:

  Set the email field with the given registered user email parameter for authentication purposes.

`getEmail()`:

  Returns the current authentication email in use.

`getStub`:

  Returns jobjRef object with the current stub field in use.

`is.connected()`:

  Check if connected to the DAVID server.

`connect()`:

  Try to establish a connection with the DAVID server using the provided email.

`getIdTypes()`:

  Returns all acceptable DAVID idTypes.

`getAllAnnotationCategoryNames()`:

  Returns all available annotation category names.

`getDefaultCategoryNames()`:

  Returns all default category names.

`getGeneListNames()`:

  Returns submitted gene list names.

`getBackgroundListNames()`:

  Returns submitted background names.

`getListName(listType=c("Gene", "Background"), position=1L)`:

  Get the name of the selected list type at a given position.

`getSpecieNames()`:

  Return specie/s of the current gene list.

`getCurrentGeneListPosition()`:

  Return the position of current gene list.

`getCurrentBackgroundListPosition()`:

  Return the position of current background list.

`getCurrentSpeciesPosition()`:

  Return current specie/s used positions for the uploaded gene list.

`setCurrentGeneListPosition(position)`:

  Use the gene list of the given position.

`setCurrentBackgroundPosition(position)`:

  Use the gene list of the given position.

`setCurrentSpecies(species)`:

  Select the specie/s of the submitted gene list to use in the analysis.

`setAnnotationCategories(categories)`:

  Select the specie/s of the submitted gene list to use in the analysis.

`addList(inputIds, idType, listName, listType=c("Gene", "Background"))`:

  Add a gene or background to the current session.

`getGeneCategoriesReport()`:

  Get the gene report categories.

`getAnnotationSummary()`:

  Generate the summary of all available annotation in DAVID in terms of percentage of gene list ids present in the category and numbers of terms where the can be found.

`getGeneListReportFile(fileName)`:

  Generate the Gene List Report a.k.a Show Gene List in DAVID website and save it into a file.

`getGeneListReport()`:

  getGeneListReport but as an R object.

`getFunctionalAnnotationChartFile(fileName, threshold=0.1, count=2L)`:

  Generate the Functional Annotation Chart Report for the selected functional categories, for the given EASE threshold and number of genes and save it to a file.

`getFunctionalAnnotationChart(...)`:

  getFunctionalAnnotationChart but as an R object.

`getClusterReportFile(fileName, type=c("Term", "Gene"), overlap=4L, initialSeed=4L, finalSeed=4L, linkage=0.5, kappa=35L)`:

  Generate the Term/Gene Cluster Report for the given configuration.

`getClusterReport(type=c("Term", "Gene"), ...)`:

  Wrapper for getClusterReportFile function.

`getFunctionalAnnotationTableFile(fileName)`:

  Generate Functional Annotation Table Report File, which is a gene-centric view of the genes and their associated annotation terms (selected only). There is no statistics applied in this report.

`getFunctionalAnnotationTable()`:

  getFunctionalAnnotationTable but as an R object.

### Limitations

1. A job with more than 3000 genes to generate gene or term cluster report will not be handled by DAVID due to resource limit.

2. No more than 200 jobs in a day from one user or computer.

3. DAVID Team reserves right to suspend any improper uses of the web service without notice.

### Author(s)

Cristobal Fresno cristobalfresno@gmail.com and Elmer A. Fernandez elmerfer@gmail.com

### 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

3. 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, Frederick, MD 21702, USA., 2009, 37, 1-13

4. 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

5. Cristobal Fresno, Elmer A. Fernandez (2013) RDAVIDWebService: a versatile R interface to DAVID, Bioinformatics, 29(21), 2810-2811., http://bioinformatics.oxfordjournals.org/content/29/21/2810.

### See Also

Other DAVIDWebService: `addList`, `addList`, `connect`, `connect`, `getAllAnnotationCategoryNames`, `getAllAnnotationCategoryNames`, `getAnnotationSummary`, `getAnnotationSummary`, `getBackgroundListNames`, `getBackgroundListNames`, `getClusterReport`, `getClusterReport`, `getClusterReportFile`, `getClusterReportFile`, `getCurrentBackgroundListPosition`, `getCurrentBackgroundListPosition`, `getCurrentGeneListPosition`, `getCurrentGeneListPosition`, `getCurrentSpeciesPosition`, `getCurrentSpeciesPosition`, `getDefaultCategoryNames`, `getDefaultCategoryNames`, `getEmail`, `getEmail`, `getFunctionalAnnotationChart`, `getFunctionalAnnotationChart`, `getFunctionalAnnotationChartFile`, `getFunctionalAnnotationChartFile`, `getFunctionalAnnotationTable`, `getFunctionalAnnotationTable`, `getFunctionalAnnotationTableFile`, `getFunctionalAnnotationTableFile`, `getGeneCategoriesReport`, `getGeneCategoriesReport`, `getGeneListNames`, `getGeneListNames`, `getGeneListReport`, `getGeneListReport`, `getGeneListReportFile`, `getGeneListReportFile`, `getIdTypes`, `getIdTypes`, `getListName`, `getListName`, `getSpecieNames`, `getSpecieNames`, `getStub`, `getStub`, `is.connected`, `is.connected`, `setAnnotationCategories`, `setAnnotationCategories`, `setCurrentBackgroundPosition`, `setCurrentBackgroundPosition(position)`, `setCurrentGeneListPosition`, `setCurrentGeneListPosition`, `setCurrentSpecies`, `setCurrentSpecies`, `setEmail`, `setEmail`, `setEmail,DAVIDWebService-method`, `summary`, `summary`, `summary`, `summary`

[Package RDAVIDWebService version 1.26.0 Index]