links: Construct hyperlinks to online resources

In aaronwolen/linkit: Create Hyperlinks to Biological Databases and Resources

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_go(): to Gene Ontology Consortium

• link_kegg(): to KEGG Pathway Database

• link_pubmed(): to PubMed based on PMID (PubMed identifier)

• link_entrez(): to NCBI's database for gene-specific information based on Entrez ID

• link_cran(): for R packages available from CRAN

• link_bioc(): for R packages available from Bioconductor

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:

• symbol: Gene symbol

• description: Gene description

• location: Cytogenetic location

NCBI PubMed:

• title: Article title

• year: Publication year

• journal: Journal title

Gene Ontology:

• name: GO term name

• definition: GO term definition

References

• Gene Ontology Consortium

• KEGG Pathway Database

• NCBI PubMed

• NCBI Gene

Examples

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

aaronwolen/linkit documentation built on Aug. 29, 2023, 5:58 a.m.