links {biolink}R Documentation

Construct hyperlinks to online resources

Description

These resource-specific functions return a hyperlink to the relevant online database/resource based on the provided identifier (id).

Usage

link_go(id, text = id, title = NULL, format = "html")

link_kegg(id, text = id, title = NULL, format = "html")

link_pubmed(id, text = id, title = NULL, format = "html")

link_entrez(id, text = id, title = NULL, format = "html")

link_cran(id, text = id, title = NULL, format = "html")

link_bioc(id, text = id, title = NULL, format = "html")

Arguments

id

valid identifier for the relevant online database

text

displayed text

title

link title, often used in tooltips

format

generate links using "html", "markdown" or "latex" syntax

Functions

Link Customization

By default the hyperlinked text is just the id, so link_pubmed("22066989") becomes 22066989. The text argument allows you to customize the hyperlinked text. To display a hyperlinked URL (e.g., https://www.r-project.org), set text = NULL.

Data Tags

For a few supported online resources, specially formatted tags can be passed to the text and title arguments to display live data obtained from the corresponding resource. For example, link_entrez("4609", text = "<symbol>"), produces MYC, displaying the gene symbol rather than the Entrez ID. We could also set title = "<description>" to produce a link that reveals the gene's description when a user hovers over the link (using a supported browser).

Currently supported data tags:

NCBI Entrez:

NCBI PubMed:

Gene Ontology:

References

Examples

link_go("GO:0005539", format = "html")
link_kegg("hsa04915", format = "html")
link_pubmed("22066989", format = "html")
link_entrez("4609", format = "html")


[Package biolink version 0.1.7 Index]