DAVIDGenes {RDAVIDWebService} | R Documentation |
Different ways to build the different DAVIDWebService's object according to the signature in use.
DAVIDGenes(object) ## S4 method for signature 'character' DAVIDGenes(object) ## S4 method for signature 'data.frame' DAVIDGenes(object) ## S4 method for signature 'DAVIDGenes' initialize(.Object, fileName) as(object, Class, strict=TRUE, ext=possibleExtends(thisClass, Class)) DAVIDFunctionalAnnotationChart(object) ## S4 method for signature 'character' DAVIDFunctionalAnnotationChart(object) ## S4 method for signature 'data.frame' DAVIDFunctionalAnnotationChart(object) ## S4 method for signature 'DAVIDFunctionalAnnotationChart' initialize(.Object, fileName) as(object, Class, strict=TRUE, ext=possibleExtends(thisClass, Class)) ## S4 method for signature 'DAVIDCluster' initialize(.Object, fileName) ## S4 method for signature 'DAVIDGeneCluster' initialize(.Object, fileName) DAVIDGeneCluster(object) ## S4 method for signature 'character' DAVIDGeneCluster(object) ## S4 method for signature 'DAVIDTermCluster' initialize(.Object, fileName) DAVIDTermCluster(object) ## S4 method for signature 'character' DAVIDTermCluster(object) ## S4 method for signature 'DAVIDFunctionalAnnotationTable' initialize(.Object, fileName) as(object, Class, strict=TRUE, ext=possibleExtends(thisClass, Class)) DAVIDFunctionalAnnotationTable(object) ## S4 method for signature 'character' DAVIDFunctionalAnnotationTable(object) ## S4 method for signature 'data.frame' DAVIDFunctionalAnnotationTable(object) ## S4 method for signature 'DAVIDGODag' initialize(.Object,funChart,type=c("BP","MF","CC"),pvalueCutoff=0.1,removeUnattached=FALSE,...) DAVIDGODag(funChart, ...) ## S4 method for signature 'DAVIDFunctionalAnnotationChart' DAVIDGODag(funChart, ...)
object |
could be a character with the file name of the .tab report or data.frame already loaded. |
fileName |
character with the file name of the .tab report to load. |
.Object |
character to use in new function call. Possible values are: "DAVIDGenes", "DAVIDFunctionalAnnotationChart" or "DAVIDCluster". |
Class |
character to use in the |
strict,ext |
see |
funChart |
DAVIDFunctionalAnnotationChart object. |
type |
character to indicate Gene Ontology main category: "BP", "MF" or "CC". |
pvalueCutoff |
numeric >0 <=1 to indicate the p-value to use as the threshold for enrichment. Default value is 0.1 |
removeUnattached |
Should unattached nodes be removed from GO DAG? Default value is FALSE. |
... |
Additional parameters for lower level constructors (initialize). |
a DAVIDWebService object according to function call:
DAVIDGenes |
object with genes description related data. |
DAVIDFunctionalAnnotationChart |
object with the respective report. |
DAVIDFunctionalAnnotationTable |
object with the respective report. |
DAVIDCluster |
Not possible to invoke as it is a Virtual class. |
DAVIDGeneCluster |
object with the respective report. |
DAVIDTermCluster |
object with the respective report. |
DAVIDGODag |
derived GOstats GO Direct Acyclic Graph from DAVIDFunctionalAnnotationChart data. |
Cristobal Fresno and Elmer A Fernandez
Other DAVIDFunctionalAnnotationChart:
DAVIDFunctionalAnnotationChart-class
,
categories
, categories
,
categories
, ids
,
ids
, ids
, ids
,
ids
, plot2D
,
plot2D
, plot2D
,
plot2D
, plot2D
,
plot2D
Other DAVIDFunctionalAnnotationTable:
DAVIDFunctionalAnnotationTable-class
,
categories
, categories
,
categories
, dictionary
,
dictionary
, genes
,
genes
, genes
,
genes
, membership
,
membership
, plot2D
,
plot2D
, plot2D
,
plot2D
, plot2D
,
plot2D
, subset
,
subset
Other DAVIDGODag: DAVIDGODag-class
,
benjaminis
, benjaminis
,
bonferronis
, bonferronis
,
counts
, counts
,
fdrs
, fdrs
,
foldEnrichments
,
foldEnrichments
, listTotals
,
listTotals
, percentages
,
percentages
, popHits
,
popHits
, popTotals
,
popTotals
, summary
,
summary
, summary
,
summary
, terms
,
terms
, universeCounts
,
universeMappedCount
,
upsideDown
, upsideDown
Other DAVIDGeneCluster:
DAVIDGeneCluster-class
,
genes
, genes
,
genes
, genes
,
ids
, ids
, ids
,
ids
, ids
,
plot2D
, plot2D
,
plot2D
, plot2D
,
plot2D
, plot2D
Other DAVIDGenes: DAVIDGenes-class
,
genes
, genes
,
genes
, genes
,
ids
, ids
, ids
,
ids
, ids
Other DAVIDTermCluster:
DAVIDTermCluster-class
, ids
,
ids
, ids
, ids
,
ids
, plot2D
,
plot2D
, plot2D
,
plot2D
, plot2D
,
plot2D
{ ##DAVIDGenes example: ##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. data(geneList1) davidGenes1<-DAVIDGenes(geneList1) ##In addition, the user can use the file name of the downloaded file report. ##Here, we need to first uncompressed the report included in the package, in ##order to load it. setwd(tempdir()) fileName<-system.file("files/geneListReport1.tab.tar.gz", package="RDAVIDWebService") untar(fileName) davidGenes1<-DAVIDGenes(untar(fileName,list=TRUE)) ##DAVIDFunctionalAnnotationChart example ##Load the Functional Annotation Chart file report for the input demo ##file 2, using data function. Then, create a DAVIDFunctionalAnnotationChart ## object using the loaded data.frame funChart2. data(funChart2) davidFunChart2<-DAVIDFunctionalAnnotationChart(funChart2) ##In addition, the user can use the file name of the downloaded file report. ##Here, we need to first uncompressed the report included in the package, in ##order to load it. setwd(tempdir()) fileName<-system.file("files/functionalAnnotationChartReport2.tab.tar.gz", package="RDAVIDWebService") untar(fileName) davidFunChart2<-DAVIDFunctionalAnnotationChart(untar(fileName, list=TRUE)) ##DAVIDFunctionalAnnotationTable example ##Load the Functional Annotation Table file report for the input demo ##file 1, using data function. Then, create a DAVIDFunctionalAnnotationTable ##object using the loaded data.frame annotationTable1. data(annotationTable1) davidFunTable1<-DAVIDFunctionalAnnotationTable(annotationTable1) ##In addition, the user can use the file name of the downloaded file report. ##Here, we need to first uncompressed the report included in the package, in ##order to load it. setwd(tempdir()) fileName<-system.file("files/annotationTableReport1.tab.tar.gz", package="RDAVIDWebService") untar(fileName) davidFunTable1<-DAVIDFunctionalAnnotationTable(untar(fileName, list=TRUE)) ##Example DAVIDGODag ##Load the Functional Annotation Chart file report for the input demo ##file 2, using data function. Then, create a DAVIDGODag object using ##Molecular Function main category of DAVIDFunctionalAnnotationChart object, ##obtained from the loaded data.frame funChart2. In addition, we have ##selected a threshold pvalue of 0.001 and removed unattached nodes, in case ##DAVID/GO.db database are not using the same version. data(funChart2) davidGODag<-DAVIDGODag(DAVIDFunctionalAnnotationChart(funChart2), type="MF", pvalueCutoff=0.001, removeUnattached=TRUE) ##DAVIDGeneCluster example: ##Load the Gene Functional Classification Tool file report for the ##input demo list 1 file to create a DAVIDGeneCluster object. setwd(tempdir()) fileName<-system.file("files/geneClusterReport1.tab.tar.gz", package="RDAVIDWebService") untar(fileName) davidGeneCluster1<-DAVIDGeneCluster(untar(fileName, list=TRUE)) ##DAVIDTermCluster example: ##Load the Gene Functional Classification Tool file report for the ##input demo file 2 to create a DAVIDGeneCluster object. setwd(tempdir()) fileName<-system.file("files/termClusterReport2.tab.tar.gz", package="RDAVIDWebService") untar(fileName) davidTermCluster2<-DAVIDTermCluster(untar(fileName, list=TRUE)) }