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\name{blastSequences}
\alias{blastSequences}
\title{
Run a blast query to NCBI for either a string or an entrez gene ID and
then return a series of MultipleAlignment objects.
}
\description{
This function sends a query to NCBI as a string of sequence or an
entrez gene ID and then returns a series of MultipleAlignment objects.
}
\usage{
blastSequences(x, database, hitListSize, filter, expect, program,
timeout=40, as=c("DNAMultipleAlignment", "data.frame", "XML"))
}
\arguments{
\item{x}{
A sequence as a character vector or an integer corresponding to an
entrez gene ID. Submit multiple sequences as a length-1 character
vector, \code{x = ">ID-1\nACATGCTA\n>ID-2\nAAACCACTT"}.
}
\item{database}{
Which NCBI database to use. If not \dQuote{blastn}, then set
\code{as="XML"}
}
\item{hitListSize}{
Number of hits to keep.
}
\item{filter}{
Sequence filter; \dQuote{L} for Low Complexity, \dQuote{R} for Human Repeats,
\dQuote{m} for Mask lookup
}
\item{expect}{
The BLAST \sQuote{expect} value above which matches will be
returned.
}
\item{program}{
Which program do you want to use for blast.
}
\item{timeout}{
Approximate maximum length of time, in seconds, to wait for a result.
}
\item{as}{
character(1) indicating whether the result from the NCBI server
should be parsed to a list of \code{DNAMultipleAlignment} instances,
represented as a \code{data.frame}, or returned as XML.
}
}
\details{
Right now the function only works for "blastn".
The NCBI URL api used by this function is documented at
\url{https://www.ncbi.nlm.nih.gov/blast/Doc/urlapi.html}
}
\value{
By default, a series of \code{DNAMultipleAlignment} (see
\code{\link[Biostrings]{MultipleAlignment-class}}
objects. Alternatively, a \code{data.frame} or XML document returned
from the NCBI server. The \code{data.frame} is a \sQuote{long form}
representation of the \sQuote{Iteration}, \sQuote{Hit} and
\sQuote{Hsp} results returned from the server. The XML document is the
result of the \code{xmlParse} function of the XML library, and follows
the format described by
\url{https://www.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.dtd} and
\url{https://www.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.mod.dtd}. }
\author{
M. Carlson
}
\examples{
## x can be an entrez gene ID
blastSequences(17702, timeout=40, as="data.frame")
if (interactive()) {
## or x can be a sequence
blastSequences(x = "GGCCTTCATTTACCCAAAATG")
## hitListSize does not promise that you will get the number of
## matches you want.. It will just try to get that many.
blastSequences(x = "GGCCTTCATTTACCCAAAATG", hitListSize="20")
}
}
|
