reutils (version 0.2.1)

content,ecitmatch-method: Extract the data content from an Entrez request

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

## S3 method for class 'ecitmatch':
content(x, as = "text")
## S3 method for class 'efetch':
content(x, as = NULL)
## S3 method for class 'egquery':
content(x, as = NULL)
## S3 method for class 'einfo':
content(x, as = NULL)
## S3 method for class 'elink':
content(x, as = NULL)
## S3 method for class 'epost':
content(x, as = NULL)
## S3 method for class 'esearch':
content(x, as = NULL)
## S3 method for class 'espell':
content(x, as = NULL)
## S3 method for class 'esummary':
content(x, as = NULL)
content(x, ...)
## S3 method for class 'eutil':
content(x, ...)

Arguments

x

An eutil object.

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 o

...

Further arguments passed on to methods.

Methods (by class)

• ecitmatch: Return PubMed IDs ifas = "parsed".
• efetch:
• egquery:
• einfo:
• elink:
• epost:
• esearch:
• espell:
• esummary:
• eutil:

See Also

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

Examples

## 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)