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

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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.

Author
Sarah Sandmann
Date of publication
None
Maintainer
Sarah Sandmann <sarah.sandmann@uni-muenster.de>
License
LGPL-3
Version
1.2.0

View on Bioconductor

Man pages

BadRegionFinder-package
\Sexpr[results=rd,stage=build]{tools:::Rd_package_title("BadRegionFinder")}
determineCoverage
Determines the coverage (recommended for whole-genome...
determineCoverageQuality
Classifies the determined coverage
determineQuantiles
Determines basewise user-defined quantiles
determineRegionsOfInterest
Determines the regions of interest
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...
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

Files in this package

BadRegionFinder/DESCRIPTION
BadRegionFinder/NAMESPACE
BadRegionFinder/NEWS
BadRegionFinder/R
BadRegionFinder/R/BadRegionFinder.R
BadRegionFinder/R/additional.R
BadRegionFinder/R/plots.R
BadRegionFinder/R/reports.R
BadRegionFinder/build
BadRegionFinder/build/partial.rdb
BadRegionFinder/build/vignette.rds
BadRegionFinder/inst
BadRegionFinder/inst/doc
BadRegionFinder/inst/doc/BadRegionFinder.R
BadRegionFinder/inst/doc/BadRegionFinder.Rnw
BadRegionFinder/inst/doc/BadRegionFinder.pdf
BadRegionFinder/inst/extdata
BadRegionFinder/inst/extdata/SampleNames.txt
BadRegionFinder/inst/extdata/SampleNames2.txt
BadRegionFinder/inst/extdata/Test2_454.bai
BadRegionFinder/inst/extdata/Test2_454.bam
BadRegionFinder/inst/extdata/Test2_ion.bai
BadRegionFinder/inst/extdata/Test2_ion.bam
BadRegionFinder/inst/extdata/Test_454.bai
BadRegionFinder/inst/extdata/Test_454.bam
BadRegionFinder/inst/extdata/Test_ion.bai
BadRegionFinder/inst/extdata/Test_ion.bam
BadRegionFinder/inst/extdata/regionsOfInterest.bed
BadRegionFinder/inst/extdata/targetRegions.bed
BadRegionFinder/inst/extdata/targetRegions2.bed
BadRegionFinder/man
BadRegionFinder/man/BadRegionFinder-package.Rd
BadRegionFinder/man/determineCoverage.Rd
BadRegionFinder/man/determineCoverageQuality.Rd
BadRegionFinder/man/determineQuantiles.Rd
BadRegionFinder/man/determineRegionsOfInterest.Rd
BadRegionFinder/man/plotDetailed.Rd
BadRegionFinder/man/plotSummary.Rd
BadRegionFinder/man/plotSummaryGenes.Rd
BadRegionFinder/man/reportBadRegionsDetailed.Rd
BadRegionFinder/man/reportBadRegionsGenes.Rd
BadRegionFinder/man/reportBadRegionsSummary.Rd
BadRegionFinder/vignettes
BadRegionFinder/vignettes/BadRegionFinder.Rnw
BadRegionFinder/vignettes/bibpaper.bib