elink: Entrez database links

In cstubben/genomes2: Genome sequencing project metadata

Description

Find links between Entrez databases at NCBI

Usage

elink(id, cmd = "neighbor_history", parse = TRUE, showURL = FALSE, ...)

Arguments

id	An EntrezHistory object or vector of Ids
cmd	Command mode
parse	Parse results into an EntrezHistory object (default) or vector of linked Ids (if cmd="neighbor"). All other cmd options return XML
showURL	display URL string
...	Other key-value pairs such as dbfrom, db, linkname passed to the elink url string

Details

See einfo to find available links

Value

Same as esearch

Note

If EntrezHistory results are the input, then the database listed in that object is used as the dbfrom key. Some additional checks are needed to catch timeout and other errors returned by the NCBI servers.

Author(s)

Chris Stubben

References

http://www.ncbi.nlm.nih.gov/books/NBK25499

Examples

## Not run: 
elink("15718680,157427902", dbfrom="protein", db="gene")
elink("15718680,157427902", dbfrom="protein", db="gene", cmd="neighbor")

# list linknames
einfo("genome", TRUE)[, 1:2]
x <- esearch("Nipah virus", "genome")
# dbfrom is set to "genome" and default link is "genome_nuccore"  
y <- elink(x, db="nuccore")
y
# Links to reference AND genbank sequence the reference was derived from
esummary(y)
# OR link to Other genomes for Species
esummary( elink(x, db="nuccore", linkname="genome_nuccore_samespecies"))

## End(Not run)

cstubben/genomes2 documentation built on May 14, 2019, 12:25 p.m.