RDAVIDWebService (version 1.10.0)

getGeneCategoriesReport: Obtain DAVID website reports

Description

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).

Usage

getGeneCategoriesReport(object)
  "getGeneCategoriesReport"(object)
  getAnnotationSummary(object)
  "getAnnotationSummary"(object)
  getGeneListReportFile(object, fileName)
  "getGeneListReportFile"(object, fileName)
  getGeneListReport(object)
  "getGeneListReport"(object)
  getFunctionalAnnotationChartFile(object, fileName, threshold=0.1, count=2L)
  "getFunctionalAnnotationChartFile"(object, fileName, threshold=0.1, count=2L)
  getFunctionalAnnotationChart(object, ...)
  "getFunctionalAnnotationChart"(object, ...)
  getClusterReportFile(object, fileName, type=c("Term", "Gene"), overlap=4L, initialSeed=4L, finalSeed=4L, linkage=0.5, kappa=35L)
  "getClusterReportFile"(object, fileName, type=c("Term", "Gene"), overlap=4L, initialSeed=4L, finalSeed=4L, linkage=0.5, kappa=35L)
  getClusterReport(object, type=c("Term", "Gene"), ...)
  "getClusterReport"(object, type=c("Term", "Gene"), ...)
  getFunctionalAnnotationTableFile(object, fileName)
  "getFunctionalAnnotationTableFile"(object, fileName)
  getFunctionalAnnotationTable(object)
  "getFunctionalAnnotationTable"(object)

Arguments

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.

Value

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:

1. Main.Category: factor with the main categories under used in the present analysis.
2. ID: integer to identify the annotation category.
3. Name: character with the name of category (the available ones in getAllAnnotationCategoryNames function).
4. X.: numeric with the percentage of the gene list ids present in the term.
5. Count: integer with the number of ids of the gene list that belong to this term.

getGeneListReportFile

data.frame with the Gene List Report with the following columns:

1. ID: character with the Gene List ID present in DAVID knowledge base, in the submitted type. If more than one ids map to the same DAVID ID, the record is a comma separated character.
2. Name: character with the name of the gene as seen in DAVID knowledge base, in a comma separated fashion (if more than one ID maps to the same DAVID ID).
3. Species: factor with the name of the Specie.

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:

1. Category: factor with the main categories under used in the present analysis.
2. Term: character with the name of the term in format id~name (if available).
3. Count: integer with the number of ids of the gene list that belong to this term.
4. X.: after converting user input gene IDs to corresponding DAVID gene ID, it refers to the percentage of DAVID genes in the list associated with a particular annotation term. Since DAVID gene ID is unique per gene, it is more accurate to use DAVID ID percentage to present the gene-annotation association by removing any redundancy in user gene list, i.e. two user IDs represent same gene.
5. PValue: numeric with the EASE Score of the term (see DAVID Help page).
6. Genes: character in comma separated style with the genes present in the term.
7. List.Total, Pop.Hits, Pop.Total: integers (in addition to Count) to build the 2x2 contingency table in order to compute the EASE Score (see DAVID Help page).
8. Fold.Enrichment: numeric with the ratio of the two proportions. For example, if 40/400 (i.e. 10%) of your input genes involved in "kinase activity" and the background information is 300/30000 genes (i.e. 1%) associating with "kinase activity", roughly 10% / 1% = 10 fold enrichment.
9. Bonferroni, Benjamini, FDR: numerics with p-value adjust different criteria (see p.adjust).

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:

1. Annotation/Gene Cluster: integer with the number of cluster.
2. EnrichmentScore: numeric with the geometric mean (in -log scale) of members p-values in a corresponding annotation cluster, is used to rank their biological significance. Thus, the top ranked annotation groups most likely have consistent lower p-values for their annotation members.
3. Members: according to the type of cluster, changes the associated data to include Gene List or Functional Chart Report (see getGeneListReport and getFunctionalAnnotationChart).

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:

1. Gene: Three Columns with the same data included in Gene List Report (ID, Gene.Name and Species) but coding for DAVID ID, i. e., comma separated character with input ids if two or more stands for the same gene.
2. Annotation: as many columns as Annotation Categories were in used. In each column, a comma separated style is use to delimitate the different terms where is reported evidence for DAVID ID record.

getFunctionalAnnotationTable:

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.

Details

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.

References

1. http://david.abcc.ncifcrf.gov/helps/functional_annotation.html#E3
2. http://david.abcc.ncifcrf.gov/helps/functional_classification.html#clustering
3. Cohen, J: A coefficient of agreement for nominal scales, Educational and Psychological Measurement, 1960, 20, 37-46.

See Also

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