CINdex: Chromosome Instability Index
Version 1.4.0

The CINdex package addresses important area of high-throughput genomic analysis. It allows the automated processing and analysis of the experimental DNA copy number data generated by Affymetrix SNP 6.0 arrays or similar high throughput technologies. It calculates the chromosome instability (CIN) index that allows to quantitatively characterize genome-wide DNA copy number alterations as a measure of chromosomal instability. This package calculates not only overall genomic instability, but also instability in terms of copy number gains and losses separately at the chromosome and cytoband level.

Browse man pages Browse package API and functions Browse package files

AuthorLei Song, Krithika Bhuvaneshwar, Yue Wang, Yuanjian Feng, Ie-Ming Shih, Subha Madhavan, Yuriy Gusev
Bioconductor views CopyNumberVariation Genetics GenomicVariation Microarray Sequencing Software aCGH
Date of publicationNone
MaintainerYuriy Gusev <yg63@georgetown.edu>
LicenseGPL (>= 2)
Version1.4.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("CINdex")

Man pages

clin.crc: Colon cancer clinical dataset
cnvgr.18.auto: Probe annotation file for Affymetrix Genome Wide Human SNP...
comp.heatmap: A comprehensive heatmap function that plots Chromosome and...
cytobands.cin: Cytoband CIN dataset
cyto.cin4heatmap: Cytoband CIN T-test output
extract.genes.in.cyto.regions: Given an input of cytobands, it outputs a list of genes that...
geneAnno: CDS gene annotation file
grl.data: Output of segmentation algorithm
hg18.ucsctrack: Human reference annotation file
run.cin.chr: Calculate chromosome CIN
run.cin.cyto: Calculate cytoband CIN
snpgr.18.auto: Probe annotation file for Affymetrix Genome Wide Human SNP...
ttest.cyto.cin.heatmap: Performs T test on cytoband level CIN data, and plots heatmap

Functions

cin.core Source code
cin.cytobands Source code
cin.standard Source code
clin.crc Man page
cnvgr.18.auto Man page
comp.heatmap Man page Source code
convert.grl.to.seg Source code
cyto.cin4heatmap Man page
cytobands.cin Man page
cytobands.cin.draw Source code
extract.genes.in.cyto.regions Man page
geneAnno Man page
grl.data Man page
hg18.ucsctrack Man page
process.probe.anno Source code
process.reference.genome Source code
run.cin.chr Man page Source code
run.cin.cyto Man page Source code
segments.to.profile Source code
snpgr.18.auto Man page
ttest.cyto.cin.heatmap Man page

Files

DESCRIPTION
NAMESPACE
R
R/cin.core.R
R/cin.cytobands.R
R/cin.standard.R
R/comp.heatmap.R
R/convert.grl.to.seg.R
R/cytobands.cin.draw.R
R/extract.genes.in.cyto.regions.R
R/heatmap.draw.R
R/plot.cytobands.R
R/process.probe.anno.R
R/process.reference.genome.R
R/profile.to.segments.R
R/run.cin.chr.R
R/run.cin.cyto.R
R/segments.to.profile.R
R/ttest.cyto.cin.heatmap.R
build
build/vignette.rds
data
data/clin.crc.RData
data/cnvgr.18.auto.RData
data/cyto.cin4heatmap.RData
data/cytobands.cin.RData
data/datalist
data/geneAnno.RData
data/grl.data.RData
data/hg18.ucsctrack.RData
data/snpgr.18.auto.RData
inst
inst/NEWS
inst/doc
inst/doc/CINdex.R
inst/doc/CINdex.Rnw
inst/doc/CINdex.pdf
inst/doc/PrepareInputData.R
inst/doc/PrepareInputData.Rmd
inst/doc/PrepareInputData.pdf
inst/unitTests
inst/unitTests/test-run.cin.chr.R
man
man/clin.crc.Rd
man/cnvgr.18.auto.Rd
man/comp.heatmap.Rd
man/cyto.cin4heatmap.Rd
man/cytobands.cin.Rd
man/extract.genes.in.cyto.regions.Rd
man/geneAnno.Rd
man/grl.data.Rd
man/hg18.ucsctrack.Rd
man/run.cin.chr.Rd
man/run.cin.cyto.Rd
man/snpgr.18.auto.Rd
man/ttest.cyto.cin.heatmap.Rd
tests
tests/RunTests.R
vignettes
vignettes/CIN_relapse_VS_nonrelapse_for_unnormalized_dendrogram.pdf
vignettes/CINdex.Rnw
vignettes/PrepareInputData.Rmd
vignettes/barplots.pdf
vignettes/biblio.bib
vignettes/chr20.png
vignettes/hg19ToHg18.over.chain
vignettes/output_chr_plots.pdf
CINdex documentation built on May 20, 2017, 10:33 p.m.