genesbyinterprodomain: Find genes containing a specified protein domain from the...
In duncantl/REuPathDB: Interface to REST API of (EuPathDB)
Description
Find genes whose predicted protein contains a domain from
the InterPro set of domain databases. You may use '*' as a wild card character. The domain matches are
identified by the InterProScan program. To learn more about InterPro see the <a href="http://www.ebi.ac.uk/interpro/tutorial.html">InterPro tutorial</a>.
<p>First choose a member database.
<p>Then begin typing the domain name, or part of it. You will
be prompted with all possible domains that match what you have typed.
<p>
For PFAM type a Pfam name, a Pfam accession or a Pfam description. Use the
<a href="http://pfam.sanger.ac.uk/family/browse?browse=top%20twenty">Pfam browser</a> to search Pfam if you are not sure.
More information on Pfam is available
<a href="http://www.sanger.ac.uk/Software/Pfam/">
here</a>.
Arguments
organism
Organism
Provide one or more values. Use comma as a delimter.
domain_database
Choose one of the constituent databases of InterPro.
domain_accession
Start typing and then choose a domain from the list of domains that come up. As you type the list gets narrowed to match only those entries that match what you have typed.
o-fields
Single valued attributes of the feature.
Provide one or more values. Use comma as a delimter.
o-tables
Multi-valued attributes of the feature.
Provide one or more values. Use comma as a delimter.
.convert
a logical value or a function that controls how the result of the method is returned. If this is a function, the character string or raw vector is passed to this function and it converts it appropriately. If this is a logical value and TRUE, then we attempt to convert the result based on its Content-Type returned by the Web server. If this is FALSE, the value from the Web server is returned as is.
.url
the URL for the Web request. This defaults to the correct value, but can be specified by the caller if the method is available at a different URL, e.g. locally or in a mirror server.
.json
a logical value controlling whether to use the JSON or the XML version of the method
Value
text/xml
text/plain
duncantl/REuPathDB documentation built on May 15, 2019, 5:28 p.m.
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Description
Find genes whose predicted protein contains a domain from the InterPro set of domain databases. You may use '*' as a wild card character. The domain matches are identified by the InterProScan program. To learn more about InterPro see the <a href="http://www.ebi.ac.uk/interpro/tutorial.html">InterPro tutorial</a>. <p>First choose a member database. <p>Then begin typing the domain name, or part of it. You will be prompted with all possible domains that match what you have typed. <p> For PFAM type a Pfam name, a Pfam accession or a Pfam description. Use the <a href="http://pfam.sanger.ac.uk/family/browse?browse=top%20twenty">Pfam browser</a> to search Pfam if you are not sure. More information on Pfam is available <a href="http://www.sanger.ac.uk/Software/Pfam/"> here</a>.
Arguments
organism |
Organism Provide one or more values. Use comma as a delimter. |
domain_database |
Choose one of the constituent databases of InterPro. |
domain_accession |
Start typing and then choose a domain from the list of domains that come up. As you type the list gets narrowed to match only those entries that match what you have typed. |
o-fields |
Single valued attributes of the feature. Provide one or more values. Use comma as a delimter. |
o-tables |
Multi-valued attributes of the feature. Provide one or more values. Use comma as a delimter. |
.convert |
a logical value or a function that controls how the result of the method is returned. If this is a function, the character string or raw vector is passed to this function and it converts it appropriately. If this is a logical value and |
.url |
the URL for the Web request. This defaults to the correct value, but can be specified by the caller if the method is available at a different URL, e.g. locally or in a mirror server. |
.json |
a logical value controlling whether to use the JSON or the XML version of the method |
Value
text/xml text/plain
R Package Documentation
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Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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