peakbound: Refine Peak Boundaries from SBC Collapsed Significant Regions
In sivarajankumar/zinba: ZINBA: Zero-Inflation Negative Binomial Algorithm

Description Usage Arguments See Also Examples

Takes SBC from bpout file line by line and determines exact peak boundaries, outputting them to a final peak file containing coordinates of collapsed and refined regions, in addition to the location of the max value in refined region and max value.

1	peakbound(bpprofile,output,pwinSize=200, winSize,quantile=.75,minscore=0)

`bpprofile`	path to file that holds matrix of overlap information generated by basecountimport
`output`	specify file name/path for output file that holds refined peaks
`winSize`	window size, default=500bp
`pWinSize`	In the peak refinement step, reduce this parameter to get more sensitivity to detect local Maximums, default is 200. This may increase false positives
`method`	method used to generate files in winlist, either mixture or pscl
`pquant`	In the peak refinement step, filters out local maximums whose height is lower than the 'pquant' quantile in the window. Use pquant=1 for selecting only the global max in a collapsed region, god for ChIP-seq datasets. Default is .75
`minscore`	minimum max height threshold for significant windows, filters out windows with max values below this point

save.

	   #FAIRE-seq with recommended parameters, no input.  
	   peakbound(bpprofile='FAIRE/faireresults.bpout',output='FAIRE/faireresults.peaks',winSize=250,pWinSize=200,pquant=1, minscore=5)