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CNprep (version 1.0)

pre-process DNA copy number (CN) data for detection of CN events

Description

The package evaluates DNA copy number data, using both their intitial 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.

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Version

Install

install.packages('CNprep')

Monthly Downloads

224

Version

1.0

License

GPL-2

Maintainer

Guoli Sun

Last Published

June 20th, 2013

Functions in CNprep (1.0)

cnpexample

Example of a boundary positions table.
annotexample

Annotation table for ROMA CGH platform and human genome version 17.
get.center

segsample

makeCNPmask

Given a set of copy-number events, create a DNA copy-number mask
CNpreprocessing

Pre-process DNA copy number (CN) data for detection of CN events.
smedmad

smedian.sample

CNprep-package

What the package does (short line) ~~ package title ~~
smedian

getz

consolidate

CNclusterNcenter

ratexample

Example of copy number log ratio data
applyCNPmask

Apply a mask to a table of copy number events.
normalComparison

weighted.median

centerprob

segexample

Example of a segmented copy number table.
normsegs

A reference set of segments
smad