Description Usage Arguments Details Value References See Also
DAVIDWebService
class methods to obtain DAVID
website reports from R. This includes the different
functionalities starting from the basic "Show Gene List"
or "Annotation Summary", to Set Enrichment Analysis using
"Functional Annotation Chart" or Modular Enrichment
Analysis using "Functional Annotation Clustering" or
"Gene Functional Classification Tool". Note that
DAVIDWebService
is a Reference class, hence invoke
it using object_name$method_name(parameters). In
addition, the user can use the S4 version style function
call (see Details).
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 | getGeneCategoriesReport(object)
## S4 method for signature 'DAVIDWebService'
getGeneCategoriesReport(object)
getAnnotationSummary(object)
## S4 method for signature 'DAVIDWebService'
getAnnotationSummary(object)
getGeneListReportFile(object, fileName)
## S4 method for signature 'DAVIDWebService'
getGeneListReportFile(object,
fileName)
getGeneListReport(object)
## S4 method for signature 'DAVIDWebService'
getGeneListReport(object)
getFunctionalAnnotationChartFile(object, fileName,
threshold=0.1, count=2L)
## S4 method for signature 'DAVIDWebService'
getFunctionalAnnotationChartFile(object,
fileName, threshold=0.1, count=2L)
getFunctionalAnnotationChart(object, ...)
## S4 method for signature 'DAVIDWebService'
getFunctionalAnnotationChart(object,
...)
getClusterReportFile(object, fileName, type=c("Term",
"Gene"), overlap=4L, initialSeed=4L, finalSeed=4L,
linkage=0.5, kappa=35L)
## S4 method for signature 'DAVIDWebService'
getClusterReportFile(object,
fileName, type=c("Term", "Gene"), overlap=4L,
initialSeed=4L, finalSeed=4L, linkage=0.5, kappa=35L)
getClusterReport(object, type=c("Term", "Gene"), ...)
## S4 method for signature 'DAVIDWebService'
getClusterReport(object,
type=c("Term", "Gene"), ...)
getFunctionalAnnotationTableFile(object, fileName)
## S4 method for signature 'DAVIDWebService'
getFunctionalAnnotationTableFile(object,
fileName)
getFunctionalAnnotationTable(object)
## S4 method for signature 'DAVIDWebService'
getFunctionalAnnotationTable(object)
|
object |
DAVIDWebService class object. |
fileName |
character with the name of the file to store the Report. |
threshold |
numeric with the EASE score (at most equal) that must be present in the category to be included in the report. Default value is 0.1. |
count |
integer with the number of genes (greater equal) that must be present in the category to be included in the report. Default value is 2. |
type |
character with the type of cluster to obtain Term/Genes. Default value "Term". |
overlap |
integer with the minimum number of annotation terms overlapped between two genes in order to be qualified for kappa calculation. This parameter is to maintain necessary statistical power to make kappa value more meaningful. The higher value, the more meaningful the result is. Default value is 4L. |
initialSeed,finalSeed |
integer with the number of genes in the initial (seeding) and final (filtering) cluster criteria. Default value is 4L for both. |
linkage |
numeric with the percentage of genes that two clusters share in order to become one. |
kappa |
integer (kappa * 100), with the minimum kappa value to be considered biological significant. The higher setting, the more genes will be put into unclustered group, which lead to higher quality of functional classification result with a fewer groups and a fewer gene members. Kappa value 0.3 starts giving meaningful biology based on our genome-wide distribution study. Anything below 0.3 have great chance to be noise. |
... |
additional parameters for getXXFile functions. |
Available functions include:
getGeneCategoriesReport
:Get the gene categories report.
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
:Generate the Gene List Report a.k.a Show Gene List in DAVID website and save it into a file.
getGeneListReport
:Generate Gene List Report a.k.a Show Gene List in DAVID website and import it as a DAVIDGenes object into R.
getFunctionalAnnotationChartFile
: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
:Generate the Functional Annotation Chart Report for the selected functional categories, for the given EASE threshold and number of genes, and import it as a DAVIDFunctionalAnnotationChart object in R.
getClusterReportFile
:Generate the Term/Gene Cluster Report for the given configuration.
getClusterReport
:Generate the Term/Gene Cluster Report for the given configuration, and import it as a DAVIDGeneCluster or DAVIDTermCluster object, according to function call.
getFunctionalAnnotationTableFile
: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
:Generate Functional Annotation Table Report and import it as a DAVIDFunctionalAnnotationTable object in R.
according to the call one of the following objects can be returned
getGeneCategoriesReport |
integer vector with the IDs of the categories. |
getAnnotationSummary |
data.frame with the annotation summary report with the following columns:
|
getGeneListReportFile |
data.frame with the Gene List Report with the following columns:
|
getGeneListReport |
Generate Gene List Report a.k.a Show Gene List in DAVID website and import it as a DAVIDGenes object in R. |
getFunctionalAnnotationChartFile |
file with the following columns:
|
getFunctionalAnnotationChart |
Generate the Functional Annotation Chart Report for the selected functional categories, for the given EASE threshold and number of genes, and import it as a DAVIDFunctionalAnnotationChart object in R. |
getClusterReportFile |
file with the following columns:
|
getClusterReport |
Generate the Term/Gene Cluster Report for the given configuration, and import it as a DAVIDGeneCluster or DAVIDTermCluster according to function call. |
getFunctionalAnnotationTableFile |
file with the following columns:
|
|
Generate Functional Annotation Table Report, which is a gene-centric view of the genes and their associated annotation terms (selected only), and import it as a DAVIDFunctionalAnnotationTable object in R. |
http://david.abcc.ncifcrf.gov/helps/functional_annotation.html#E3
http://david.abcc.ncifcrf.gov/helps/functional_classification.html#clustering
Cohen, J: A coefficient of agreement for nominal scales, Educational and Psychological Measurement, 1960, 20, 37-46.
p.adjust
and fisher.test
Other DAVIDWebService:
DAVIDWebService-class
,
addList
, addList
,
connect
, connect
,
getAllAnnotationCategoryNames
,
getAllAnnotationCategoryNames
,
getBackgroundListNames
,
getBackgroundListNames
,
getCurrentBackgroundListPosition
,
getCurrentBackgroundListPosition
,
getCurrentGeneListPosition
,
getCurrentGeneListPosition
,
getCurrentSpeciesPosition
,
getCurrentSpeciesPosition
,
getDefaultCategoryNames
,
getDefaultCategoryNames
,
getEmail
, getEmail
,
getGeneListNames
,
getGeneListNames
, 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
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