CNVPanelizer: Reliable CNV detection in targeted sequencing applications

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A method that allows for the use of a collection of non-matched normal tissue samples. Our approach uses a non-parametric bootstrap subsampling of the available reference samples to estimate the distribution of read counts from targeted sequencing. As inspired by random forest, this is combined with a procedure that subsamples the amplicons associated with each of the targeted genes. The obtained information allows us to reliably classify the copy number aberrations on the gene level.

Author
Cristiano Oliveira [aut], Thomas Wolf [aut, cre], Albrecht Stenzinger [ctb], Volker Endris [ctb], Nicole Pfarr [ctb], Benedikt Brors [ths], Wilko Weichert [ths]
Date of publication
None
Maintainer
Thomas Wolf <thomas_wolf71@gmx.de>
License
GPL-3
Version
1.4.0

View on Bioconductor

Man pages

Background
Background
BedToGenomicRanges
BedToGenomicRanges
BootList
BootList
CNVPanelizer-package
Reliable CNV detection in targeted sequencing applications
CombinedNormalizedCounts
CombinedNormalizedCounts
IndexMultipleBams
IndexMultipleBams
PlotBootstrapDistributions
PlotBootstrapDistributions
ReadCountsFromBam
ReadCountsFromBam
ReadXLSXToList
ReadXLSXToList
referenceReadCounts
Reference sample data
ReportTables
ReportTables
sampleReadCounts
Test sample data
WriteListToXLSX
WriteListToXLSX

Files in this package

CNVPanelizer/DESCRIPTION
CNVPanelizer/NAMESPACE
CNVPanelizer/NEWS
CNVPanelizer/R
CNVPanelizer/R/FolderAnalysis_functions.R
CNVPanelizer/R/SyntheticData.R
CNVPanelizer/README.md
CNVPanelizer/build
CNVPanelizer/build/vignette.rds
CNVPanelizer/data
CNVPanelizer/data/referenceReadCounts.RData
CNVPanelizer/data/sampleReadCounts.RData
CNVPanelizer/inst
CNVPanelizer/inst/doc
CNVPanelizer/inst/doc/CNVPanelizer.R
CNVPanelizer/inst/doc/CNVPanelizer.Rnw
CNVPanelizer/inst/doc/CNVPanelizer.pdf
CNVPanelizer/inst/extdata
CNVPanelizer/inst/extdata/regions.bed
CNVPanelizer/inst/unitTests
CNVPanelizer/inst/unitTests/test_testing.R
CNVPanelizer/man
CNVPanelizer/man/Background.Rd
CNVPanelizer/man/BedToGenomicRanges.Rd
CNVPanelizer/man/BootList.Rd
CNVPanelizer/man/CNVPanelizer-package.Rd
CNVPanelizer/man/CombinedNormalizedCounts.Rd
CNVPanelizer/man/IndexMultipleBams.Rd
CNVPanelizer/man/PlotBootstrapDistributions.Rd
CNVPanelizer/man/ReadCountsFromBam.Rd
CNVPanelizer/man/ReadXLSXToList.Rd
CNVPanelizer/man/ReportTables.Rd
CNVPanelizer/man/WriteListToXLSX.Rd
CNVPanelizer/man/referenceReadCounts.Rd
CNVPanelizer/man/sampleReadCounts.Rd
CNVPanelizer/run_tests.R
CNVPanelizer/tests
CNVPanelizer/tests/runTests.R
CNVPanelizer/vignettes
CNVPanelizer/vignettes/CNVPanelizer.Rnw
CNVPanelizer/vignettes/CNVPanelizer.bib