entrez_link {rentrez} | R Documentation |
Get links to datasets related to records from an NCBI database
Description
Discover records related to a set of unique identifiers from
an NCBI database. The object returned by this function depends on the value
set for the cmd
argument. Printing the returned object lists the names
, and provides a brief description, of the elements included in the object.
Usage
entrez_link(
dbfrom,
web_history = NULL,
id = NULL,
db = NULL,
cmd = "neighbor",
by_id = FALSE,
config = NULL,
...
)
Arguments
dbfrom |
character Name of database from which the Id(s) originate |
web_history |
a web_history object |
id |
vector with unique ID(s) for records in database |
db |
character Name of the database to search for links (or use "all" to
search all databases available for |
cmd |
link function to use. Allowed values include
|
by_id |
logical If FALSE (default) return a single
|
config |
vector configuration options passed to httr::GET |
... |
character Additional terms to add to the request, see NCBI documentation linked to in references for a complete list |
Value
An elink object containing the data defined by the cmd
argument
(if by_id=FALSE) or a list of such object (if by_id=TRUE).
file XMLInternalDocument xml file resulting from search, parsed with
xmlTreeParse
References
https://www.ncbi.nlm.nih.gov/books/NBK25499/#_chapter4_ELink_
See Also
config
for available configs
entrez_db_links
Examples
## Not run:
pubmed_search <- entrez_search(db = "pubmed", term ="10.1016/j.ympev.2010.07.013[doi]")
linked_dbs <- entrez_db_links("pubmed")
linked_dbs
nucleotide_data <- entrez_link(dbfrom = "pubmed", id = pubmed_search$ids, db ="nuccore")
#Sources for the full text of the paper
res <- entrez_link(dbfrom="pubmed", db="", cmd="llinks", id=pubmed_search$ids)
linkout_urls(res)
## End(Not run)