Description Usage Arguments See Also Examples
Implements model selection procedure. Getsigwindows() is called using modelselect=TRUE to determine the best fitting model on a subset of the data. Each model's BIC is calculated and is outputted to a file at location "loc". The model with the lowest score is then chosen. All possible models given a set of starting covariates are considered when selecttype="complete". A much faster model selection procedure (selecttype="dirty") fixes the zero-inflation component to have no covariates and first selects best covariates for the background and enriched components. After these covariates are selected, the best zero-inflation covariates are chosen.
1 | covariateselect(inputfile, outputfile)
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inputfile |
Path to file in the current directory map.list, which contains the names of the chromosome specific binary files in the mappability directory. Each chromosome binary file contains a score at every base corresponding to the number of times a given k-mer occurs in the genome, originating from that base; downloaded from repository or self generated |
outputfile |
single wig file where results should be printed |
save
.
1 2 3 4 | #Corresponding to FAIRE example in run.zinba:
covariateselect(inputfile='mappabilitylist.txt', outputfile='mappability.wig')
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