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RDAVIDWebService (version 1.10.0)

DAVIDWebService-class: 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.

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.

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.

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