Utility functions for UCSC bin indexing system manipulation
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A vector of integers. A set of ranges.
A integer vector of length 1. A coordinate range.
Name of bin column. Default: "bin".
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).
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.
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
than to use this function directly.
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 *
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
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