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
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)
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 |
... |
Further arguments passed on to methods. |
as |
Type of output: |
Methods (by class)
-
eutil
: Access the data content from aneutil
object. -
ecitmatch
: Return PubMed IDs ifas = "parsed"
. -
efetch
: Access the data content from anefetch
request. -
egquery
: Access the data content from anegquery
request. -
einfo
: Access the data content from aneinfo
request. -
elink
: Access the data content from anelink
request. -
epost
: Access the data content from anepost
request. -
esearch
: Access the data content from anesearch
request. -
espell
: Access the data content from anespell
request. -
esummary
: Access the data content from anesummary
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)
## 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)