genomes (version 2.16.0)

efetch: Entrez database downloads

Description

Retrieve Entrez database records at NCBI in a variety of formats

Usage

efetch(id, db = "pubmed", rettype = "", retmode = "text", showURL = FALSE, destfile, ...)

Arguments

id

An EntrezHistory object or vector of Ids

db

An Entrez database, default pubmed

rettype

Retrieval type, see note for details

retmode

Retrieval mode, see note for details

showURL

display URL string

destfile

location to save downloaded file using download.file. If missing, the url is loaded into R using readLines

...

Other key-value pairs passed to the efetch url string, e.g seq_stop

Value

References

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

Examples

## Not run: 
# # abstracts from recent bioC articles - use ids to limit the number 
# x <- esearch("bioconductor[TITLE]", usehistory="n", retmax=5, reldate=360 )
# x
# efetch(x, rettype="abstract")
# # only first 500 bases
# efetch( esearch( "Yersinia pestis CO92[ORGN] AND refseq[FILTER] AND plasmid[Filter]", "nuccore"), rettype="fasta", seq_stop=500)
# efetch(16082679, "nuccore", "fasta")
# ## End(Not run)