efetch.batch: Retrieve batches of data records in the requested format from...

In gschofl/rentrez: An R interface to the NCBI EUtilities

Description

efetch.batch retrieves large data sets from NCBI in batches.

Usage

  efetch.batch(id, chunk_size = 200, rettype = NULL,
    retmode = NULL, retmax = NULL, strand = NULL,
    seq_start = NULL, seq_stop = NULL, complexity = NULL)

Arguments

id	(Required) List of UIDs provided (via the Entrez History server) by an esearch, epost or elink object.
chunk_size	Number of records downloaded as a batch (default: 200; maximum: 500).
rettype	A character string specifying the record view returned, such as 'abstract' or 'medline' from PubMed, or 'gp' or 'fasta' from protein. See here for allowed values for each database.
retmode	A character string specifying the data format of the records returned, such as plain text, XML, or asn.1. See here for allowed values for each database.
retmax	Total number of records from the input set to be retrieved.
strand	Strand of DNA to retrieve. (1: plus strand, 2: minus strand)
seq_start	First sequence base to retrieve.
seq_stop	Last sequence base to retrieve.
complexity	Data content to return. (0: entire data structure, 1: bioseq, 2: minimal bioseq-set, 3: minimal nuc-prot, 4: minimal pub-set)

Details

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

Value

An efetch object.

Examples

## Download a large set of records (>500)

# Download all human ncRNAs in FASTA format
query <- "human[orgn] and biomol ncrna[prop]"

# Let's check how many there are
esearch(query, "nucleotide", rettype="count")

# upload the GIs to the history server
ncrna <- esearch(query, "nucleotide", usehistory=TRUE)
ncrna

## Not run
## download ncRNAs in batch mode
# fasta <- efetch.batch(id=ncrna, chunk_size=200, rettype="fasta")
# write(fasta, "~/human_small_nuclear_rna.fasta")

gschofl/rentrez documentation built on May 17, 2019, 8:53 a.m.