qblast: Do a BLAST search using the QBLAST URL API

In gschofl/blastr: A wrapper for NCBI Blast

Description

Do a BLAST search using the QBLAST URL API

Usage

qblast(query, exec = "megablast", db = "nt", outfmt = "xml",
  max_hits = 20, entrez_query = "", evalue = 10, ..., .params = list(),
  update_time = 4)

Arguments

query	Query sequences as path to a FASTA file, an XStringSet object, or a character vector.
db	The database to BLAST against.
outfmt	Output format. One of 'xml' or 'tabular'. See Details.
max_hits	The maximum number of hits to return.
entrez_query	An Entrez query used to limit the results.
evalue	Expectation value threshold for saving hits.
...	The name-value pairs of parameters passed on to the QBLAST URL API.
.params	A named list of parameters passed on to the QBLAST URL API.
update_time	How often to poll the blast server for results.
program	The blast application to use. One of 'megablast' (default), 'blastn', 'blastp', 'rpsblast', blastx', 'tblastn', 'tblastx'.
db	Blast database name. (defaults: 'nt').

Value

A blastReport-class object.

See Also

Other blast functions: blastn, blastn_short, blastn_short, dc_megablast, dc_megablast, megablast, megablast; blastp, blastp_short, blastp_short; blastx; makeblasttdb; rpsblast; tblastn; tblastx

Examples

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gschofl/blastr documentation built on May 17, 2019, 8:52 a.m.