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\name{binning-utils}
\alias{binFromCoordRange}
\alias{binRangesFromCoordRange}
\alias{binRestrictionString}
\title{UCSC bin indexing system utility functions}
\description{Utility functions for UCSC bin indexing system manipulation}
\usage{
binFromCoordRange(starts, ends)
binRangesFromCoordRange(start, end)
binRestrictionString(start, end, field="bin")
}
\arguments{
\item{starts, ends}{
A vector of integers. A set of ranges.
}
\item{start, end}{
A integer vector of length 1. A coordinate range.
}
\item{field}{
Name of bin column. Default: "bin".
}
}
\value{
For \code{binFromCoordRange}, it returns the bin number
that should be assigned to a feature spanning the given range.
Usually it is used when creating a database for the features.
For \code{binRangesFromCoordRange}, it returns the set of bin ranges
that overlap a given coordinate range.
It is usually used to find out the bins overlapped with a range.
For SQL query, it is more convenient to use \code{binRestrictionString}
than to use this function directly.
For \code{binRestrictionString}, it returns a string to be used
in the WHERE section of a SQL SELECT statement
that is to select features overlapping a certain range.
* USE THIS WHEN QUERYING A DB *
}
\details{
The UCSC bin indexing system was initially suggested by Richard Durbin and
Lincoln Stein to speed up the SELECT of a SQL query for the rows overlapping
with certain genome coordinate.
The system first used in UCSC genome browser is
described by Kent et. al. (2002).
}
\references{
Kent, W. J., Sugnet, C. W., Furey, T. S., Roskin, K. M., Pringle,
T. H., Zahler, A. M., & Haussler, A. D. (2002).
The Human Genome Browser at UCSC. Genome Research, 12(6),
996-1006. doi:10.1101/gr.229102
\url{http://genomewiki.ucsc.edu/index.php/Bin_indexing_system}
}
\author{
Ge Tan
}
\examples{
binFromCoordRange(starts=c(10003, 1000000), ends=c(10004, 1100000))
binRangesFromCoordRange(start=10000, end=2000000)
binRestrictionString(start=10000, end=2000000, field="bin")
}
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