content: Extract the data content from an Entrez request

In reutils: Talk to the NCBI EUtils

Description

There are five ways to access data returned by an Entrez request: as a character string (as = "text"), as a textConnection (as = "textConnection"), as an XMLInternalDocument (as = "xml") or json object (as = "json") (depending on the retmode with which the request was performed), or parsed into a native R object, e.g. a list or a data.frame (as = "parsed").

Usage

content(x, ...)

## S4 method for signature 'eutil'
content(x, ...)

## S4 method for signature 'ecitmatch'
content(x, as = "text")

## S4 method for signature 'efetch'
content(x, as = NULL)

## S4 method for signature 'egquery'
content(x, as = NULL)

## S4 method for signature 'einfo'
content(x, as = NULL)

## S4 method for signature 'elink'
content(x, as = NULL)

## S4 method for signature 'epost'
content(x, as = NULL)

## S4 method for signature 'esearch'
content(x, as = NULL)

## S4 method for signature 'espell'
content(x, as = NULL)

## S4 method for signature 'esummary'
content(x, as = NULL)

Arguments

x	An eutil object.
...	Further arguments passed on to methods.
as	Type of output: "text", "xml", "json", "textConnection", or "parsed". content attempts to figure out the most appropriate output type, based on the retmode of the object.

Methods (by class)

• eutil: Access the data content from an eutil object.

• ecitmatch: Return PubMed IDs if as = "parsed".

• efetch: Access the data content from an efetch request.

• egquery: Access the data content from an egquery request.

• einfo: Access the data content from an einfo request.

• elink: Access the data content from an elink request.

• epost: Access the data content from an epost request.

• esearch: Access the data content from an esearch request.

• espell: Access the data content from an espell request.

• esummary: Access the data content from an esummary request.

See Also

einfo, esearch, esummary, efetch, elink, epost, egquery, espell, ecitmatch.

Examples

## Not run: 
## einfo() defaults to retmode 'xml'
e <- einfo()

## automatically return data as an 'XMLInternalDocument'.
if (e$no_errors()) {
  content(e)

  ## return the XML data as character string.
  cat(content(e, "text"))

  ## return DbNames parsed into a character vector.
  content(e, "parsed")
}

## return data as a JSON object
e2 <- einfo(db = "gene", retmode = "json")
if (e2$no_errors()) {
  content(e2)
}

## return a textConnection to allow linewise reading of the data.
x <- efetch("CP000828", "nuccore", rettype = "gbwithparts", retmode = "text")
con <- content(x, as = "textConnection")
readLines(con, 2)
close(con)

## End(Not run)

Example output

Warning: CurlError: Could not resolve host: eutils.ncbi.nlm.nih.gov
Warning: CurlError: Could not resolve host: eutils.ncbi.nlm.nih.gov
Warning: CurlError: Could not resolve host: eutils.ncbi.nlm.nih.gov
[1] ""

reutils documentation built on May 1, 2019, 9:15 p.m.