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

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

AuthorVolker Hovestadt, Marc Zapatka
Date of publicationNone
MaintainerVolker Hovestadt <conumee@hovestadt.bio>
LicenseGPL (>= 2)
Version1.8.0

View on Bioconductor

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
CNV.create_bins Man page
[,CNV.data,ANY,ANY,ANY-method Man page
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,data.frame-method Man page
CNV.load,matrix-method Man page
CNV.load,MethylSet-method Man page
CNV.load,numeric-method Man page
CNV.merge_bins Man page
CNV.segment Man page
CNV.segment,CNV.analysis-method Man page
CNV.write Man page
CNV.write,CNV.analysis-method Man page
coef,CNV.analysis-method Man page
detail_regions Man page
exclude_regions Man page
names<-,CNV.analysis-method Man page
names,CNV.analysis-method Man page
names<-,CNV.data-method Man page
names,CNV.data-method Man page
read.450k.url Man page
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

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.