geneVServer: Shiny module server for select-filter of genes or gene...

In avucoh/DIVE: Data Integration and Visual Exploration

Shiny module server for select-filter of genes or gene products

Description

Implement augmented select-filter interface for genes powered by mygene

Usage

geneVServer(id)

Arguments

id	Character ID for specifying namespace, see shiny::NS.

Details

With the help of the mygene API, this provides an interface for reasonably flexible ways to get select some subset of genes. The first problem for a simple selection is that genomics data often requires mapping across different database IDs and accessions, e.g. between NCBI gene IDs, HUGO gene symbols, Ensembl, or to a protein product (Uniprot accessions), all of which are constantly being updated so that IDs become deprecated/obsolete. The second problem is that, aside from being able to use any database ID, one might want to use genomic coordinates or even Gene Ontology references. The end return should be whatever gene IDs the application requires, but what should be provided to the user to make their selection? This implements three entryways:

• The main select loads the preferred gene IDs stored locally by the application.

• A query field powered by the mygene API to do translations using the most current data.

• A gene list upload option to upload a gene list (one gene per line).

The return can be passed in to the parameter selected in the multiVServer module.

Value

A vector of standard gene symbols.

See Also

Other geneV functions: geneVUI()

avucoh/DIVE documentation built on Aug. 29, 2023, 6:02 p.m.