###################
*bed.avglengths*
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calculates windowed mean fragment length

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description
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``bed.avglengths`` calculates mean fragment length for all non-overlapping windows.

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usage
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::

  bed.avglengths ( databedfile , targetfile , windowsize=1000000 , genome=TRUE , fraglenoutfile="default" , numfragoutfile="default")


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arguments
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===========================      ===============================================================================================================================================================================================================
 Main options                     Description
===========================      ===============================================================================================================================================================================================================
**databedfile**                        string defining bed file name of intervals to be parsed.
**targetfile**                     character vector of length 1 specifying the path to file specifying either chromosome sizes of the genome (if genome=TRUE) or a bed file of regions of interest if genome=FALSE (e.g. Sequence Capture regions).
**windowsize**                     size of windows (in bp) for fragment statistics to be calculated.
**genome**                         Boolean indicating whether to process the whole genome (TRUE), and targetfile indicates chromosomes, or specific regions of interest (FALSE), where targetfile is a bed file of regions.
**fraglenoutfile**                 Name of the file to write mean fragment length information.
**numfragoutfile**                 Name of the file to write number of fragments per window information.
===========================      ===============================================================================================================================================================================================================


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output
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``bed.avglengths`` generates bedgraph files of the mean fragment length and number of overlapping fragments with one line for each non-overlapping window of size provided by the user..

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examples
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Calculated mean fragment length per megabase
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.. highlight:: r

::

 > bed.avglengths ( "MNase-seq-fragments.bed" ,genomefile = "/path/to/genomefile/hg19_chrom.sizes", genome=TRUE , windowsize=1000000 )