DNAcopy: DNA copy number data analysis
Version 1.50.1

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

Browse man pages Browse package API and functions Browse package files

AuthorVenkatraman E. Seshan, Adam Olshen
Bioconductor views CopyNumberVariation Microarray
Date of publicationNone
MaintainerVenkatraman E. Seshan <seshanv@mskcc.org>
LicenseGPL (>= 2)
Version1.50.1
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("DNAcopy")

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

Functions

CNA Man page Source code
DNAcopy Man page
changepoints Man page Source code
changepoints.prune Man page Source code
changepoints.sdundo Man page Source code
coriell Man page
cytoBand Man page
default.DNAcopy.bdry Man page
exon.changepoint Man page Source code
exon.segment Man page Source code
getbdry Man page Source code
glFrequency Man page Source code
inflfact Man page Source code
onLoad Source code
plot.DNAcopy Man page Source code
plotSample Man page Source code
print.CNA Man page Source code
print.DNAcopy Man page Source code
segment Man page Source code
segments.p Man page Source code
segments.summary Man page Source code
smooth.CNA Man page Source code
smooth.data Man page
subset.CNA Man page Source code
subset.DNAcopy Man page Source code
trimmed.variance Man page Source code
zoomIntoRegion Man page Source code

Files

DESCRIPTION
NAMESPACE
R
R/DNAcopyMethods.R
R/changepoints.R
R/exonsegment.R
R/getbdry.R
R/glFrequency.R
R/plotSample.R
R/segment.R
R/segmentp.R
R/segmentsummary.R
R/zoomIntoRegion.R
R/zzz.R
build
build/vignette.rds
chrom-lengths
data
data/coriell.rda
data/cytoBand.tab
data/default.DNAcopy.bdry.R
demo
demo/00Index
demo/DNAcopy.R
inst
inst/CHANGES
inst/benchmark
inst/benchmark/benchmark,20090610,segment.R
inst/doc
inst/doc/DNAcopy.R
inst/doc/DNAcopy.Rnw
inst/doc/DNAcopy.pdf
man
man/CNA.Rd
man/DNAcopy-internal.Rd
man/DNAcopy.Rd
man/coriell.Rd
man/cytoBand.Rd
man/exon.segment.Rd
man/getbdry.Rd
man/glFrequency.Rd
man/plot.DNAcopy.Rd
man/plotSample.Rd
man/segment.Rd
man/segments.p.Rd
man/segments.summary.Rd
man/smooth.CNA.Rd
man/subset.CNA.Rd
man/subset.DNAcopy.Rd
man/zoomIntoRegion.Rd
src
src/cbsWtstats.f
src/cbststats.f
src/changepoints-wtd.f
src/changepoints.f
src/esegment.f
src/flchoose.c
src/fphyper.c
src/fpnorm.c
src/getbdry.f
src/prune.f
src/rshared.c
src/segmentp.f
src/smoothCNA.f
src/tailprobs.f
tests
tests/redundancy,20090610,segment.R
vignettes
vignettes/DNAcopy.Rnw
vignettes/DNAcopy.bib
DNAcopy documentation built on May 20, 2017, 10:31 p.m.