formatDAVIDResult {DAVIDQuery} | R Documentation |
These functions attempt to format the character table result
returned by DAVID.
formatDAVIDResult(result, verbose=FALSE) formatAnnotationReport(result) formatGeneReport(result) formatGeneReportFull(result) formatList(result) formatGene2Gene(result)
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. |
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.
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. |
<id> |
The identifier(s) in the query. The name is whatever the id type was. |
<other items> |
Items produced for the input, specified by the annot arg of the query. |
<gene name> |
Using the same ID type as the type argument of DAVIDQuery() . |
Gene Name |
Self-explanatory. |
Species |
Self-explanatory. |
Gene Name |
Self-explanatory. |
Species |
Self-explanatory. |
<other items> |
The union of items produced for the input identifiers (generically called "genes" in DAVID). (The set of attributes is not fixed.) |
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
|
As of this writing, the tool choices corresponding to most Functional Annotation tools cannot be handled by this package.