# BadRegionFinder: an R/Bioconductor package for identifying regions with bad coverage

## Documentation for package ‘BadRegionFinder’ version 1.4.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

BadRegionFinder-package | BadRegionFinder: an R/Bioconductor package for identifying regions with bad coverage
Bad Coverage | BadRegionFinder: an R/Bioconductor package for identifying regions with bad coverage
BadRegionFinder | BadRegionFinder: an R/Bioconductor package for identifying regions with bad coverage
Coverage Classifier | BadRegionFinder: an R/Bioconductor package for identifying regions with bad coverage
determine Coverage Quality | Classifies the determined coverage
determine Quantiles | Determines basewise user-defined quantiles
determine Regions Of Interest | Determines the regions of interest
determineCoverage | Determines the coverage (recommended for whole-genome analyses)
determineCoverageQuality | Classifies the determined coverage
determineQuantiles | Determines basewise user-defined quantiles
determineRegionsOfInterest | Determines the regions of interest
plot Detailed | Plots a more detailed overview of the coverage quality
plot Summary | Plots a summary of the coverage quality
plot Summary Genes | Plots a summary of the coverage quality concerning the genes only
plotDetailed | Plots a more detailed overview of the coverage quality
plotSummary | Plots a summary of the coverage quality
plotSummaryGenes | Plots a summary of the coverage quality concerning the genes only
report Bad Regions Detailed | Gives a detailed report on the coverage quality
report Bad Regions Genes | Sums up the coverage quality on a gene basis
report Bad Regions Summary | Sums up the coverage quality
reportBadRegionsDetailed | Gives a detailed report on the coverage quality
reportBadRegionsGenes | Sums up the coverage quality on a gene basis
reportBadRegionsSummary | Sums up the coverage quality