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BadRegionFinder (version 1.0.0)

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

Description

BadRegionFinder is a package for identifying regions with a bad, acceptable and good coverage in sequence alignment data available as bam files. The whole genome may be considered as well as a set of target regions. Various visual and textual types of output are available.

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Version

Version

1.0.0

License

LGPL-3

Maintainer

Sarah Sandmann

Last Published

February 15th, 2017

Functions in BadRegionFinder (1.0.0)

determineCoverageQuality

Classifies the determined coverage
determineQuantiles

Determines basewise user-defined quantiles
plotSummary

Plots a summary of the coverage quality
determineRegionsOfInterest

Determines the regions of interest
plotSummaryGenes

Plots a summary of the coverage quality concerning the genes only
reportBadRegionsGenes

Sums up the coverage quality on a gene basis
determineCoverage

Determines the coverage (recommended for whole-genome analyses)
BadRegionFinder-package

\Sexpr[results=rd,stage=build]{tools:::Rd_package_title("#1")}BadRegionFinderBadRegionFinder: an R/Bioconductor package for identifying regions with bad coverage
reportBadRegionsDetailed

Gives a detailed report on the coverage quality
plotDetailed

Plots a more detailed overview of the coverage quality
reportBadRegionsSummary

Sums up the coverage quality