binning-utils {CNEr} | R Documentation

## 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

`starts, ends` | A vector of integers. A set of ranges.
`start, end` | A integer vector of length 1. A coordinate range.
`field` | Name of bin column. Default: "bin".

### 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).

### Value

For `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 `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 `binRestrictionString` than to use this function directly.

For `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 *

### Author(s)

Ge Tan

### 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

http://genomewiki.ucsc.edu/index.php/Bin_indexing_system

### Examples

      binFromCoordRange(starts=c(10003, 1000000), ends=c(10004, 1100000))
      binRangesFromCoordRange(start=10000, end=2000000)
      binRestrictionString(start=10000, end=2000000, field="bin")

[Package CNEr version 1.18.1 Index]