bed.intersect¶
calculate overlap between two sets of intervals
description¶
bed.intersect is a wrapper function for ‘bedtools intersect’, which calculates the overlap between two sets of genomic intervals.
usage¶
bed.intersect ( a , b , extraargs = "-u" )
arguments¶
| Main options | Description |
|---|---|
| a | string defining file name of bed file A. Each feature in A is compared to B in search of overlaps. |
| b | string defining file name of bed file B. |
| extraargs | extra arguments to be used in bedtools intersect ( see http://bedtools.readthedocs.org/en/latest/content/tools/intersect.html ) |
output¶
bed.intersect by default (extraargs = “-u”) will “write original A entry once if any overlaps found in B. In other words, just report the fact at least one overlap was found in B.” bed.intersect will return the file name of the resulting file, which will have the syntax [a-file]_x_[b-file].bed