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

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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.

Author
Alex Krasnitz, Guoli Sun
Date of publication
2014-12-31 18:26:36
Maintainer
Guoli Sun <guolisun87@gmail.com>
License
GPL-2
Version
2.0

View on CRAN

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.

Files in this package

CNprep
CNprep/NAMESPACE
CNprep/data
CNprep/data/ratexample.rda
CNprep/data/cnpexample.rda
CNprep/data/segexample.rda
CNprep/data/datalist
CNprep/data/normsegs.rda
CNprep/data/annotexample.rda
CNprep/R
CNprep/R/normalComparison.R
CNprep/R/smad.R
CNprep/R/breakIntoGaps.R
CNprep/R/smedmad.R
CNprep/R/CNclusterNcenter.R
CNprep/R/breakIntoCNPs.chrom.R
CNprep/R/consolidate.R
CNprep/R/centerprob.R
CNprep/R/smedian.sample.R
CNprep/R/containment.indicator.R
CNprep/R/getz.R
CNprep/R/applyCNPmask.R
CNprep/R/smedian.R
CNprep/R/get.center.R
CNprep/R/weighted.median.R
CNprep/R/makeCNPmask.R
CNprep/R/segsample.R
CNprep/R/makeCNPmask.chrom.R
CNprep/R/CNpreprocessing.R
CNprep/MD5
CNprep/DESCRIPTION
CNprep/man
CNprep/man/annotexample.Rd
CNprep/man/segexample.Rd
CNprep/man/normsegs.Rd
CNprep/man/makeCNPmask.Rd
CNprep/man/applyCNPmask.Rd
CNprep/man/CNpreprocessing.Rd
CNprep/man/cnpexample.Rd
CNprep/man/ratexample.Rd