basecountimport: Import SBC (basecounts) Given Coordinate File
In sivarajankumar/zinba: ZINBA: Zero-Inflation Negative Binomial Algorithm

Description Usage Arguments See Also

Calculates the SBC (basecounts) from a specified basecount file for a given set of merged significant windows, given a threshold level and the results from getsigwindows().

1 2	basecountimport(inputfile,winlist,threshold=.01,method='pscl',printFullOut=0, outputfile,twobitfile,chromosome='all'

`inputfile`	path to basecount track containing SBPC information for the entire genome, generated by basealigncount()
`winlist`	path to files outputted from getsigwindows()
`outputfile`	path to where file of extracted basecounts should be placed
`chromosome`	which chromosomes in coordinate file to get basecounts for. Default is all.
`threshold`	threshold for signfiicant windows corresponding to method used (mixture vs pscl)
`printFullOut`	specifies the file format ouputted from getsigwindows, where 1 correspondinds to output of full dataset with posterior enrichment probability results, 0 corresponds to only genomic coordinates and posterior probabilities
`method`	method used to generate files in winlist, either mixture or pscl
`twobitfile`	path to current build of human genome in .2bit format
`outputfile`	specify file name/path for temporary file that holds matrix of overlap information generated for peak refinement