convertmappability: Determine Best Sets of Covariates to Model Each Component

In sivarajankumar/zinba: ZINBA: Zero-Inflation Negative Binomial Algorithm

Description

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.

Usage

covariateselect(inputfile, outputfile)

Arguments

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

See Also

save.

Examples

#Corresponding to FAIRE example in run.zinba:
covariateselect(inputfile='mappabilitylist.txt',  outputfile='mappability.wig')
   
          

sivarajankumar/zinba documentation built on May 29, 2019, 10:11 p.m.