CNprep: Pre-process DNA Copy Number (CN) Data for Detection of CN Events
Version 2.0

This package evaluates DNA copy number data, using both their initial form (copy number as a noisy function of genomic position) and their approximation by a piecewise-constant function (segmentation), for the purpose of identifying genomic regions where the copy number differs from the norm.

AuthorAlex Krasnitz, Guoli Sun
Date of publication2014-12-31 18:26:36
MaintainerGuoli Sun <guolisun87@gmail.com>
LicenseGPL-2
Version2.0
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("CNprep")

Popular man pages

annotexample: Annotation table for ROMA CGH platform and human genome...
cnpexample: Example of a boundary positions table.
CNpreprocessing: Pre-process DNA copy number (CN) data for detection of CN...
makeCNPmask: Given a set of copy-number events, create a DNA copy-number...
normsegs: A reference set of segments
ratexample: Example of copy number log ratio data
segexample: Example of a segmented copy number table.
See all...

All man pages Function index File listing

Man pages

annotexample: Annotation table for ROMA CGH platform and human genome...
applyCNPmask: Apply a mask to a table of copy number events.
cnpexample: Example of a boundary positions table.
CNpreprocessing: Pre-process DNA copy number (CN) data for detection of CN...
makeCNPmask: Given a set of copy-number events, create a DNA copy-number...
normsegs: A reference set of segments
ratexample: Example of copy number log ratio data
segexample: Example of a segmented copy number table.

Functions

CNclusterNcenter Source code
CNpreprocessing Man page Source code
annotexample Man page
applyCNPmask Man page Source code
breakIntoCNPs.chrom Source code
breakIntoGaps Source code
centerprob Source code
cnpexample Man page
consolidate Source code
containment.indicator Source code
get.center Source code
getz Source code
makeCNPmask Man page Source code
makeCNPmask.chrom Source code
normalComparison Source code
normsegs Man page
ratexample Man page
segexample Man page
segsample Source code
smad Source code
smedian Source code
smedian.sample Source code
smedmad Source code
weighted.median Source code

Files

NAMESPACE
data
data/ratexample.rda
data/cnpexample.rda
data/segexample.rda
data/datalist
data/normsegs.rda
data/annotexample.rda
R
R/normalComparison.R
R/smad.R
R/breakIntoGaps.R
R/smedmad.R
R/CNclusterNcenter.R
R/breakIntoCNPs.chrom.R
R/consolidate.R
R/centerprob.R
R/smedian.sample.R
R/containment.indicator.R
R/getz.R
R/applyCNPmask.R
R/smedian.R
R/get.center.R
R/weighted.median.R
R/makeCNPmask.R
R/segsample.R
R/makeCNPmask.chrom.R
R/CNpreprocessing.R
MD5
DESCRIPTION
man
man/annotexample.Rd
man/segexample.Rd
man/normsegs.Rd
man/makeCNPmask.Rd
man/applyCNPmask.Rd
man/CNpreprocessing.Rd
man/cnpexample.Rd
man/ratexample.Rd
CNprep documentation built on May 19, 2017, 12:19 p.m.

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