conumee: Enhanced copy-number variation analysis using Illumina DNA methylation arrays
Version 1.10.0

This package contains a set of processing and plotting methods for performing copy-number variation (CNV) analysis using Illumina 450k or EPIC methylation arrays.

Browse man pages Browse package API and functions Browse package files

AuthorVolker Hovestadt, Marc Zapatka
Bioconductor views CopyNumberVariation DNAMethylation MethylationArray Microarray Normalization Preprocessing QualityControl Software
Date of publicationNone
MaintainerVolker Hovestadt <conumee@hovestadt.bio>
LicenseGPL (>= 2)
Version1.10.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("conumee")

Man pages

CNV.analysis-class: CNV.analysis class
CNV.anno-class: CNV.anno class
CNV.bin: CNV.bin
CNV.check: CNV.check
CNV.create_anno: CNV.create_anno
CNV.create_bins: CNV.create_bins
CNV.data-class: CNV.data class
CNV.detail: CNV.detail
CNV.detailplot: CNV.detailplot
CNV.detailplot_wrap: CNV.detailplot_wrap
CNV.fit: CNV.fit
CNV.genomeplot: CNV.genomeplot
CNV.load: CNV.load
CNV.merge_bins: CNV.merge_bins
CNV.process: CNV.process
CNV.segment: CNV.segment
CNV.write: CNV.write
detail_regions: detail_regions
exclude_regions: exclude_regions
read.450k.url: read.450k.url
tbl_ucsc: tbl_ucsc
tcgaBRCA.sentrix2name: tcgaBRCA.sentrix2name

Functions

CNV.analysis-class Man page
CNV.anno-class Man page
CNV.bin Man page
CNV.bin,CNV.analysis-method Man page
CNV.check Man page
CNV.check,CNV.data-method Man page
CNV.create_anno Man page Source code
CNV.create_bins Man page Source code
CNV.data-class Man page
CNV.detail Man page
CNV.detail,CNV.analysis-method Man page
CNV.detailplot Man page
CNV.detailplot,CNV.analysis-method Man page
CNV.detailplot_wrap Man page
CNV.detailplot_wrap,CNV.analysis-method Man page
CNV.fit Man page
CNV.fit,CNV.data,CNV.data,CNV.anno-method Man page
CNV.genomeplot Man page
CNV.genomeplot,CNV.analysis-method Man page
CNV.load Man page
CNV.load,GenomicRatioSet-method Man page
CNV.load,MethylSet-method Man page
CNV.load,data.frame-method Man page
CNV.load,matrix-method Man page
CNV.load,numeric-method Man page
CNV.merge_bins Man page Source code
CNV.process Man page
CNV.process,integer,integer,CNV.data,CNV.anno-method Man page
CNV.segment Man page
CNV.segment,CNV.analysis-method Man page
CNV.write Man page
CNV.write,CNV.analysis-method Man page
[,CNV.data,ANY,ANY,ANY-method Man page
coef,CNV.analysis-method Man page
cumsum0 Source code
curl Source code
detail_regions Man page
exclude_regions Man page
names,CNV.analysis-method Man page
names,CNV.data-method Man page
names<-,CNV.analysis-method Man page
names<-,CNV.data-method Man page
read.450k.url Man page Source code
show,CNV.analysis-method Man page
show,CNV.anno-method Man page
show,CNV.data-method Man page
tbl_ucsc Man page
tcgaBRCA.sentrix2name Man page

Files

.BBSoptions
DESCRIPTION
NAMESPACE
R
R/annotation.R
R/classes.R
R/data.R
R/load.R
R/output.R
R/process.R
R/sysdata.rda
README.md
TODO
build
build/vignette.rds
data
data/detail_regions.rda
data/exclude_regions.rda
data/tcgaBRCA.sentrix2name.rda
inst
inst/CITATION
inst/NEWS
inst/doc
inst/doc/conumee.R
inst/doc/conumee.Rmd
inst/doc/conumee.html
inst/extdata
inst/extdata/detail_regions.bed
inst/extdata/exclude_regions.bed
man
man/CNV.analysis-class.Rd
man/CNV.anno-class.Rd
man/CNV.bin.Rd
man/CNV.check.Rd
man/CNV.create_anno.Rd
man/CNV.create_bins.Rd
man/CNV.data-class.Rd
man/CNV.detail.Rd
man/CNV.detailplot.Rd
man/CNV.detailplot_wrap.Rd
man/CNV.fit.Rd
man/CNV.genomeplot.Rd
man/CNV.load.Rd
man/CNV.merge_bins.Rd
man/CNV.process.Rd
man/CNV.segment.Rd
man/CNV.write.Rd
man/detail_regions.Rd
man/exclude_regions.Rd
man/read.450k.url.Rd
man/tbl_ucsc.Rd
man/tcgaBRCA.sentrix2name.Rd
vignettes
vignettes/TCGA-AR-A1AU_figure.vh20150223.png
vignettes/biomed-central.csl
vignettes/conumee.Rmd
vignettes/conumee.bib
conumee documentation built on May 20, 2017, 9:48 p.m.