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

---

Documentation for package ‘BadRegionFinder’ version 1.30.0

• 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