elink: elink
In gschofl/rentrez: An R interface to the NCBI EUtilities

Description Usage Arguments Details Value Class hierarchy for elink Generics with methods for elink Slots Examples

“elink” is an S4 class that provides a container for data retrived by calls to the NCBI ELink utility.

elink generates a list of UIDs in a specified Entrez database that are linked to a set of input UIDs in either the same or another database. For instance, the ELink utility can find Entrez gene records linked to records in Entrez Protein.

  elink(id, dbFrom = NULL, dbTo = NULL, linkname = NULL,
    usehistory = FALSE, cmd = "neighbor",
    correspondence = FALSE, query_key = NULL,
    WebEnv = NULL, term = NULL, holding = NULL,
    datetype = NULL, reldate = NULL, mindate = NULL,
    maxdate = NULL)

`id`	(Required) A character vector of UIDs.
`dbFrom`	Initial database containing the UIDs in the input list.
`dbTo`	Destination database from which to retrieve linked UIDs. If not provided links will be sought in the database containing the input UIDs.
`linkname`	Name of the Entrez link to retrieve. Every link in Entrez is given a name of the form 'dbFrom_dbTo_subset'.
`usehistory`	If `TRUE` search results are stored directly in the user's Web environment so that they can be used in subsequents calls to `esummary` or `efetch`.
`cmd`	ELink command mode (default: 'neighbor'). See Details.
`correspondence`	if `TRUE` correspondence between query UIDs and destination UIDs is preserved.
`query_key`	Query key.
`WebEnv`	Web Environment.
`term`	Search query to limit the output set of linked UIDs.
`holding`	Name of LinkOut provider.
`datetype`	Type of date to limit the search. One of 'mdat' (modification date), 'pdat' (publication date) or 'edat' (Entrez date).
`reldate`	umber of days back for which search items are returned.
`mindate`	Minimum date of search range. Format YYYY/MM/DD.
`maxdate`	Maximum date of search range. Format YYYY/MM/DD.

See the official online documentation for NCBI's EUtilities for additional information.

If dbTo and dbFrom are set to the same database, ELink will return neighbors within that database.

Elink commands (cmd) specify the function that elink will perform. Available commands are:

"neighbor" (Default) ELink returns a set of UIDs in dbTo linked to the input UIDs in dbFrom.
"neighbor_score" ELink returns a set of UIDs within the same database as the input UIDs along with similarity scores.
"neighbor_history" ELink posts the output UIDs to the Entrez History server and returns a query_key and WebEnv parameter. Alternatively this is achieved by setting usehistory = TRUE
"acheck" ELink lists all links available for a set of UIDs.
"ncheck" ELink checks for the existence of links within the same database for a set of UIDs.
"lcheck" Elink checks for the existence of external links (LinkOuts) for a set of UIDs.
"llinks" For each input UID, ELink lists the URLs and attributes for the LinkOut providers that are not libraries.
"llinkslib" For each input UID, ELink lists the URLs and attributes for all LinkOut providers including libraries.
"prlinks" ELink lists the primary LinkOut provider for each input UID.

An elink instance.

Super classes:

eutil

[
content
count
database
idList
linkSet
queryKey
show
webEnv

url: A character vector containing the query URL.
error: Any error or warning messages parsed from the output of the call submitted to Entrez.
content: A character vector holding the unparsed contents of a request to Entrez.
idList: An object of class idList
databaseTo: An object of class character
command: An object of class character
queryKey: An object of class integer
webEnv: An object of class character
linkSet: A list containing the linked data.

## Find related data through ELink #########################################

# Example: find a set of pubmed IDs linked to nucleotide GIs
gis <- c("84785887","84785899","84785907","84785905","84785889")
rv <- elink(gis, "nucleotide", "pubmed")
rv

# Fetch the XML records for the linked articles
efetch(rv)

# Example: Check whether two nucleotide sequences have any LinkOut providers.
gis <- c("84785887","84785899")
rv <- elink(gis, "nucleotide", cmd="lcheck")
rv

# Example: Find publication linked to a protein sequence
a <- esearch("Chlamydia and cpaf", "protein")
a
l <- elink(a[1], dbTo="pubmed")
l
efetch(l)