bg.map¶
map bedGraph scores to genomic intervals
description¶
bg.map generates a bedGraph file by performing calculations on bedGraph intervals within other genomic intervals. For each genomic interval in ‘bedfile’, bg.map will perform ‘operation’ on all overlapping scores in ‘bgfile’.
usage¶
bg.map ( bgfile, bedfile, operation="mean" , windowsize=25, stepsize=windowsize, filler=0 , printzero=TRUE )
arguments¶
| Main options | Description |
|---|---|
| bgfile | a string defining the bedGraph file name to perform calculations on |
| bedfile | a string defining the file of intervals within which to perform calculations of the bedGraph intervals. |
| operation | a string defining the operation to perform on bedGraph intervals overlapping each ‘bedfile’ interval. See http://bedtools.readthedocs.org/en/latest/content/tools/map.html for other operations. |
| windowsize | positive integer indicating the size of windows (in bp) in ‘bedfile’. Only needs to be defined if windowsize > stepsize. |
| stepsize | positive integer indicating the distances between intervals (in bp) in ‘bedfile’. Only needs to be defined if windowsize > stepsize. |
| filler | a string or number defining the score to assign windows with no overlapping bedGraph intervals. Default is ‘0’. |
| printzero | a boolean value indicating if windows with a value of calculated value of zero should be printed. Default is TRUE. |
output¶
bg.map generates a bedGraph file by performing calculations on bedGraph intervals within other genomic intervals. For each genomic interval in ‘bedfile’, bg.map will perform ‘operation’ on all overlapping scores in ‘bgfile’. The output bedGraph will have identical intervals to ‘bedfile’, but with the calculated values in column 4.
examples¶
perform a sliding-window average of a bedGraph file with 100-bp windows at 10-bp step-sizes¶
make windows of your microarray data
> w100s10 <- bed.makewindows ( "MNase-CHIP.bg" , windowsize = 100 , stepsize = 10 )
perform a sliding-window average
> bg.map ( "MNase-CHIP.bg" , w100s10 , windowsize = 100 , stepsize = 10 )