DNAcopy: DNA copy number data analysis

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Implements the circular binary segmentation (CBS) algorithm to segment DNA copy number data and identify genomic regions with abnormal copy number.

Author
Venkatraman E. Seshan, Adam Olshen
Date of publication
None
Maintainer
Venkatraman E. Seshan <seshanv@mskcc.org>
License
GPL (>= 2)
Version
1.48.0

View on Bioconductor

Man pages

CNA
Create 'Copy Number Array' data object
coriell
Array CGH data set of Coriell cell lines
cytoBand
Cytogenic band data
DNAcopy
Results of segmenting a CNA data object
DNAcopy-internal
Internal DNAcopy functions
exon.segment
Binary segmentation of exon data.
getbdry
Sequential stopping boundary
glFrequency
Additional summary measured for the segments
plot.DNAcopy
Plot the data and results from segment of a CNA object
plotSample
Plot the data and results from segmentation for a single...
segment
Genome Segmentation Program
segments.p
p-values for the change-points
segments.summary
Additional summary measured for the segments
smooth.CNA
Smooth a 'Copy Number Array' data object
subset.CNA
Subset a 'Copy Number Array' data object
subset.DNAcopy
Subset a DNAcopy data object
zoomIntoRegion
Zoomed in view of genomic region

Files in this package

DNAcopy/DESCRIPTION
DNAcopy/NAMESPACE
DNAcopy/R
DNAcopy/R/DNAcopyMethods.R
DNAcopy/R/changepoints.R
DNAcopy/R/exonsegment.R
DNAcopy/R/getbdry.R
DNAcopy/R/glFrequency.R
DNAcopy/R/plotSample.R
DNAcopy/R/segment.R
DNAcopy/R/segmentp.R
DNAcopy/R/segmentsummary.R
DNAcopy/R/zoomIntoRegion.R
DNAcopy/R/zzz.R
DNAcopy/build
DNAcopy/build/vignette.rds
DNAcopy/chrom-lengths
DNAcopy/data
DNAcopy/data/coriell.rda
DNAcopy/data/cytoBand.tab
DNAcopy/data/default.DNAcopy.bdry.R
DNAcopy/demo
DNAcopy/demo/00Index
DNAcopy/demo/DNAcopy.R
DNAcopy/inst
DNAcopy/inst/CHANGES
DNAcopy/inst/benchmark
DNAcopy/inst/benchmark/benchmark,20090610,segment.R
DNAcopy/inst/doc
DNAcopy/inst/doc/DNAcopy.R
DNAcopy/inst/doc/DNAcopy.Rnw
DNAcopy/inst/doc/DNAcopy.pdf
DNAcopy/man
DNAcopy/man/CNA.Rd
DNAcopy/man/DNAcopy-internal.Rd
DNAcopy/man/DNAcopy.Rd
DNAcopy/man/coriell.Rd
DNAcopy/man/cytoBand.Rd
DNAcopy/man/exon.segment.Rd
DNAcopy/man/getbdry.Rd
DNAcopy/man/glFrequency.Rd
DNAcopy/man/plot.DNAcopy.Rd
DNAcopy/man/plotSample.Rd
DNAcopy/man/segment.Rd
DNAcopy/man/segments.p.Rd
DNAcopy/man/segments.summary.Rd
DNAcopy/man/smooth.CNA.Rd
DNAcopy/man/subset.CNA.Rd
DNAcopy/man/subset.DNAcopy.Rd
DNAcopy/man/zoomIntoRegion.Rd
DNAcopy/src
DNAcopy/src/cbsWtstats.f
DNAcopy/src/cbststats.f
DNAcopy/src/changepoints-wtd.f
DNAcopy/src/changepoints.f
DNAcopy/src/esegment.f
DNAcopy/src/flchoose.c
DNAcopy/src/fphyper.c
DNAcopy/src/fpnorm.c
DNAcopy/src/getbdry.f
DNAcopy/src/prune.f
DNAcopy/src/rshared.c
DNAcopy/src/segmentp.f
DNAcopy/src/smoothCNA.f
DNAcopy/src/tailprobs.f
DNAcopy/tests
DNAcopy/tests/redundancy,20090610,segment.R
DNAcopy/vignettes
DNAcopy/vignettes/DNAcopy.Rnw
DNAcopy/vignettes/DNAcopy.bib