content: Extract the data content from an Entrez request

Description Usage Arguments Methods (by class) See Also Examples

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

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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)

See Also

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

Examples

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## 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)

gschofl/reutils documentation built on Dec. 9, 2018, 1:27 a.m.