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*bed.coverage*
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calculate interval densities in windows

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description
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``bed.coverage`` counts the number genomic intervals in one bed file that overlap at each genomic interval in another bed file.

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usage
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::

  bed.coverage ( bedfile , windowbed , windowsize=25 , stepsize=windowsize , scalar="rpm" )


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arguments
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===========================      ===============================================================================================================================================================================================================
 Main options                     Description
===========================      ===============================================================================================================================================================================================================
**bedfile**                         string defining the bed file name to count the intervals within 'windowbed' intervals.
**windowbed**                       string defining the bed file name containing intervals within which to count overlapping 'bedfile' intervals.
**windowsize**                      size of windows (in bp) in 'windowbed'. Only needs to be defined if windowsize > stepsize.
**stepsize**                        distances between intervals (in bp) in 'windowbed'. Only needs to be defined if windowsize > stepsize.
**scalar**                          number to multiply interval counts by. Default is "rpm", which multiplies the coverage to report intervals per million.
===========================      ===============================================================================================================================================================================================================


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output
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``bed.coverage`` generates a bedGraph file counting the number of intervals in 'bedfile' that overlap with the intervals in 'windowbed'.
The resulting bedGraph file will contain the first three columns of the 'windowbed' file and the counts of overlapping intervals in 'bedfile' in the fourth column.
If the intervals in 'windowbed' overlap, ``bed.coverage`` can reduce the size of these intervals if 'windowsize' and 'stepsize' are defined.
This must be done in order to generate bigWig files for the UCSC genome browser.

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examples
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calculate the density of reads in bed format in 100-bp nonoverlapping intervals across the genome.
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.. highlight:: r

make a bed of 100-bp nonoverlapping intervals in the human genome

::

 > windows <- bed.makewindows ( "/path/to/genomefile" , windowsize = 100 , genome = TRUE )

generate a bedGraph of read densities

::

 > bed.coverage ( "MNaseSeqFragments" , windows )


create a dyad-density bedGraph (aka frenters) of MNase-seq data within probed regions using 100-bp windows at 10-bp step sizes
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create 100-bp windows at 10-bp step-sizes within probed regions

::

 > bed.makewindows ( "seqcapregions.bed" , windowsize=100 , stepsize=10 , sort.ranges = "-100,100" )

generate a bed of fragment centers

::

 > MNaseSeqCenters <- bed.centers ( "MNaseSeqFragments.bed" )

generate a bedGraph of dyad densities

::

 > bed.coverage ( "MNaseSeqCenters.bed" , seqcapwindows , windowsize=100 , stepsize = 10)