|
Name
|
Description
|
Default
|
|
Query parameters:
|
|
qFile
|
File of query gene ids and/or symbols.
|
|
|
qIds
|
List of query gene ids and/or symbols. Contents of qFile and qIds
are combined. qFile and qIds may contain only ids, symbols, whitespace
and commas.
|
No defaults. qIds or qFile is required.
|
|
uFile
|
File of universe ids and/or symbols.
|
|
|
uIds
|
List of universe ids and/or symbols. Contents of uFile and uIds
are combined. uFile and uIds may contain only ids, symbols, whitespace
and commas. This option applies only if scoring = "pvals".
|
Default is the IDs of all annotated objects.
|
|
scoring
|
Method of scoring: pvals or percents.
|
pvals
|
|
pThresh
|
Pruning threshold.
|
1
|
|
cThresh
|
Collapsing threshold.
|
10
|
|
Output parameters:
|
|
outDir
|
Directory where output files go. All output files are written
to this directory.
|
The current directory.
|
|
outFileRoot
|
Root name of output files. Output file names have the form:
rootname.ontologyname.format. If outFileRoot contains the
character '@', it is replaced by a digit string that guarantees
uniqueness within the directory. For example, if outFileRoot == "VLAD@",
then the output files for a given run might be: VLAD63114.process.jpg,
VLAD63114.function.jpg, VLAD63114.component.jpg, etc.
|
VLAD@
|
|
outRptFormat
|
Output format for report files. Either 'html' or 'text'.
|
If no format is specified, no reports are generated
|
|
outImgFormat
|
Output format for images. Can be anything that Graphviz recognizes. The most
common are: jpg, png, gif.
|
If no format is specified, no images are generated.
Either outRptFormat or outImgFormat (or both) must be specified.
|
|
Ontology parameters:
|
|
ontologies
|
Which ontologies to show. Combinations of: process, function, component.
Order of output matches the order given here.
|
Show all. (Order is arbitrary.)
|
|
ontologyLoader
|
Name of loader class: MGIVocLoader or OboLoader. Depending on the loader,
other parameters become relevant. If loader is MGIVocLoader, you must be sure
to add an appropriate JDBC driver to your CLASSPATH.
|
OboLoader
|
|
If ontologyLoader == OboLoader:
|
|
oboFile
|
Name of .obo file.
|
None. Required if ontologyLoader == oboLoader.
|
|
If ontologyLoader == MGIVocLoader:
|
|
jdbcDriver
|
Name of JDBC driver class
|
com.sybase.jdbc2.jdbc.SybDriver
|
|
jdbcProtocol
|
The protocol spoken by the driver
|
jdbc:sybase:Tds
|
|
jdbcServer
|
Name of MGI database SQL server
|
gondor.informatics.jax.org
|
|
jdbcPort
|
Port number
|
4025
|
|
jdbcDatabase
|
Name of MGI database on server
|
mgd
|
|
jdbcUser
|
Name of user for sql login
|
mgd_public
|
|
jdbcPassword
|
Password for sql login
|
mgdpub
|
|
Annotation data parameters:
|
|
dbAnnotationDir
|
Directory holding annotation files.
|
The current directory.
|
|
db
|
Whose annotations to use. The name of a database, e.g., mgi, fb, sgd, etc.
|
None.
|
|
dbAnnotationFile
|
The annotation file. If specified, overrides dbAnnotationDir.
|
If unspecified, looks for a file named "gene_association.[db]"
in the directory named by dbAnnotationDir.
|
|
dbFilter
|
Set of evidence codes to exclude.
|
Nothing filtered.
|
|
Other installation parameters:
|
|
vladHome
|
Directory where Vlad is installed. This variable is set by the installation
process, so you shouldn't have to worry about it.
|
None. Required.
|
|
graphVizDir
|
GraphViz installation directory.
|
None. Required. This variable is set by the installation
process, so you shouldn't have to worry about it.
|
|
outURL
|
URL equivalent of outDir. This is needed for running Vlad as a CGI, as it
has to generate URLs rather than file paths.
|
|
|
ontologyURL
|
URL template of ontology browser. Used for linking ontology terms to browser page.
|
http://www.godatabase.org/cgi-bin/go.cgi?query=%s&view=details
|
|
dbURL
|
A URL template for generating links from an annotated object to
a database report for that object.
|
None.
|
|
dbURLFile
|
File of URL templates for generating links from an annotated object to
a database report for that object. If this option is used, you must
also specify the db parameter.
|
URLs.rcd
|
Parameter Definitions