esummary: esummary - downloading Document Summaries

Description Usage Arguments Details Value See Also Examples

View source: R/esummary.R

Description

esummary performs calls to the NCBI ESummary utility to retrieve document summaries (DocSums) for a list of primary UIDs or for a set of UIDs stored in the user's web environment (using the Entrez History server).

Usage

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esummary(uid, db = NULL, retstart = 1, retmax = 10000,
  querykey = NULL, webenv = NULL, retmode = "xml", version = "2.0")

Arguments

uid

(Required) List of UIDs provided either as a character vector, as an esearch or elink object, or by reference to a Web Environment and a query key obtained directly from objects returned by previous calls to esearch, epost or elink. If UIDs are provided as a plain character vector, db must be specified explicitly, and all of the UIDs must be from the database specified by db.

db

(Required only when id is a character vector of UIDs) Database from which to retrieve DocSums.

retstart

Numeric index of the first DocSum to be retrieved (default: 1).

retmax

Total number of DocSums from the input set to be retrieved (maximum: 10,000).

querykey

An integer specifying which of the UID lists attached to a user's Web Environment will be used as input to efetch. (Usually obtained drectely from objects returned by previous esearch, epost or elink calls.)

webenv

A character string specifying the Web Environment that contains the UID list. (Usually obtained directely from objects returned by previous esearch, epost or elink calls.)

retmode

Retrieval mode. (default: 'xml', alternative: 'json')

version

If "2.0" esummary will retrieve version 2.0 ESummary XML output.

Details

See the official online documentation for NCBI's EUtilities for additional information.

Value

An esummary object.

See Also

content, getUrl, getError, database.

Examples

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## Retrieve the Document Summary information for a set of
## UIDs frome the Nuccore datanase.
ds <- esummary(c("1060721643", "1060721620", "1060721618"), "nuccore")
ds

## Not run: 
## parse the XML into a data frame
df <- content(ds, "parsed")
df

## use XPath expressions to extract nodes of interest
ds['//TaxId/text()']

## End(Not run)

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