bed.avglengths¶
calculates windowed mean fragment length
description¶
bed.avglengths calculates mean fragment length for all non-overlapping windows.
usage¶
bed.avglengths ( databedfile , targetfile , windowsize=1000000 , genome=TRUE , fraglenoutfile="default" , numfragoutfile="default")
arguments¶
| 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. |
output¶
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..