cghMCR: Find chromosome regions showing common gains/losses
Version 1.34.0

This package provides functions to identify genomic regions of interests based on segmented copy number data from multiple samples.

Browse man pages Browse package API and functions Browse package files

AuthorJ. Zhang and B. Feng
Bioconductor views CopyNumberVariation Microarray
Date of publicationNone
MaintainerJ. Zhang <jzhang@jimmy.harvard.edu>
LicenseLGPL
Version1.34.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("cghMCR")

Man pages

cghMCR: The constructor for the cghMCR class
cghMCR-class: Class "cghMCR" is a S4 class for the identification of...
mergeMCRProbes: A function that appends probe ids to a data frame containing...
methods: Methods for Function colnames/rownames in Package 'cghMCR'
plot.DNAcopy: A function to plot the original data along with the segments...
SGOL-class: Class "SGOL" reprents segments of gain or loss across samples

Functions

MCR Man page
MCR,cghMCR-method Man page
SGOL Man page Source code
SGOL-class Man page
[,SGOL-method Man page
[-methods Man page
adjustSegments Source code
alignGenes Source code
cghMCR Man page Source code
cghMCR-class Man page
colnames,SGOL-method Man page
colnames-methods Man page
drawSegs Source code
dropCNP Source code
dropGenes Source code
findLocus Source code
findMCR Source code
findSpan Source code
getAdjustments Source code
getAlteredSegs Source code
getChromLength Source code
getChromMargin Source code
getGEOI Source code
getLineData Source code
getLocus Source code
getMCR Source code
getPotentialMCR Source code
getSGOL Source code
getSegData Source code
getSegments Man page
getSegments,marrayNorm-method Man page
getSegments,marrayRaw-method Man page
gol Man page
gol,SGOL-method Man page
highlightChrom Source code
markChrom Source code Source code
mergeChrom Source code
mergeGOL Source code
mergeMCRProbes Man page Source code
mergeSegs Source code
mergeStartNEnd Source code
method,SGOL-method Man page
plot Man page
plot,ANY-method Man page
plot,SGOL,ANY-method Man page
plot,SGOL-method Man page
plot,methods Man page
plot.DNAcopy Man page Source code
plot.MCR Source code
plotSGOL Source code
rownames,SGOL-method Man page
rownames-methods Man page
segData Man page
showMCR Source code
showSegment Source code
sortByChromNLoc Source code
splitSegByMean Source code
splitSegments Source code
threshold,SGOL-method Man page
topGenes Source code

Files

DESCRIPTION
NAMESPACE
NAMESPACEBACK
R
R/cghMCR.R
R/mcrFunctions.R
build
build/vignette.rds
data
data/segData.rda
inst
inst/doc
inst/doc/findMCR.R
inst/doc/findMCR.Rnw
inst/doc/findMCR.pdf
inst/sampleData
inst/sampleData/TCGA-06-0881-01A-02D-0387-02-short.txt
inst/sampleData/TCGA-12-0818-01A-01D-0387-02-short.txt
inst/sampleData/TCGA-12-0827-01A-01D-0387-02-short.txt
man
man/SGOL-class.Rd
man/cghMCR-class.Rd
man/cghMCR.Rd
man/mergeMCRProbes.Rd
man/methods.Rd
man/plot.DNAcopy.Rd
vignettes
vignettes/findMCR.Rnw
vignettes/segplot.eps
vignettes/segplot.png
vignettes/sgolPlot.eps
vignettes/sgolPlot.png
cghMCR documentation built on May 20, 2017, 10:33 p.m.