DAVIDQuery (version 1.32.0)

formatDAVIDResult: Format the character table returned by DAVID.

Description

These functions attempt to format the character table result returned by DAVID.

Usage

formatDAVIDResult(result, verbose=FALSE)
formatAnnotationReport(result)
formatGeneReport(result)
formatGeneReportFull(result)
formatList(result)
formatGene2Gene(result)

Arguments

result

Character table returned by DAVID.

verbose

If TRUE, print tool. Warn if tool=="geneReportFull" that the result will be returned invisibly due to its size.

Value

For tool=="geneAnnotationReport", a list, one component for each element in the ids arg. Each component has subcomponents

Gene Name

Self-explanatory.

Species

Self-explanatory.

The identifier(s) in the query. The name is whatever the id type was.

Items produced for the input, specified by the annot arg of the query.

For tool=="geneReport" or tool=="list", a character matrix with column names scraped from DAVIDQueryResult, usually:

Using the same ID type as the type argument of DAVIDQuery().

Gene Name

Self-explanatory.

Species

Self-explanatory.

In addition, for tool=="geneReport", the first line of the returned output is saved as an attribute before discarding it.For tool=="geneReportFull", a list, one component for each element in the ids arg. Each component has subcomponents

Gene Name

Self-explanatory.

Species

Self-explanatory.

The union of items produced for the input identifiers (generically called "genes" in DAVID). (The set of attributes is not fixed.)

For tool=="formatGene2Gene", a list with one component for each Functional Group. Each component has components

median

See DAVID documentation.

geo

See DAVID documentation.

diagram

An attempt to parse the fourth column of the Functional Group line of the input. See DAVID documentation and consult the DAVID team.

details

A data frame with columns

gene

"gene" as identified in the ids arg to DAVIDQuery

geneName

gene name

url

The URL for the Gene Report page at NIAID.

As of this writing, the tool choices corresponding to most Functional Annotation tools cannot be handled by this package.

Details

formatDAVIDResult switches out to one of formatGeneReport, formatGeneReportFull, formatGene2Gene, or formatList, depending on the tool argument of DAVIDQuery() used to specify what query report to do. The tool argument is passed as an attribute attached to result.

WARNINGS: Not all values of tool have an associated format.

These format utilities are not guaranteed to work correctly for all combinations of inputs into DAVIDQuery(), or to continue to work correctly if or when the DAVID API changes. If results appear incorrect, one can use the option DAVIDQuery(formatIt=FALSE) to see the unformatted output, and/or paste DAVIDQuery(details=TRUE)[firstURL] into a browser.

In the case of formatGene2Gene, the gene column of the details component might not always contain a single identifier.