estswithgeneoverlap: Find ESTs in a Library that do or do not overlap with a gene.

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

Description

Find ESTs that Overlap a Gene. <br /><br />EST's have been clustered/assembled into "DoTS Assemblies" which represent consensus sequences of overlapping EST's and mRNA's. NOTE: You can query for DoTS Assemblies directly by using the <a href="showQuestion.do?questionFullName=AssemblyQuestions.AssembliesWithGeneOverlap">Assemblies by Gene Overlap Query</a>.

Arguments

libraryIdGenes	Select a clone library. Provide one or more values. Use comma as a delimter.
bp_overlap_gte	Overlap of expressed sequence tag (EST) alignments with annotated genes is a useful approach to verify gene predictions. In general, the specificity of this evidence is proportional to the overlap length.
overlapOrNot	Select yes to return only those EST alignments that are consistent. We define define consistent as having >= 95% identity (the majority have >= 99%) and aligning the EST sequence in a manner that is consistent with a gene model. Ie, there can be gaps (representing introns) in the target genomic sequence but not in the EST query.
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

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duncantl/REuPathDB documentation built on May 15, 2019, 5:28 p.m.