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 |
save
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