genesbypdbsimilarity: Find genes whose protein product has high BLAST similarity to...

In duncantl/REuPathDB: Interface to REST API of (EuPathDB)

Description

Find genes whose protein product has high BLAST similarity to a chain of a <a href="http://www.rcsb.org/pdb">Protein Data Bank (PDB)</a> structure. Specify one or more organisms whose genes to retrieve; one or more clades of organisms whose PDB records should be considered; and a p-value exponent cutoff.

Arguments

organism	Organism Provide one or more values. Use comma as a delimter.
clades	Select one or more clades. Provide one or more values. Use comma as a delimter.
pvalue_cutoff	Only consider BLAST similarities with a P-value less than ten to the given power.
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.