ChAMP: Chip Analysis Methylation Pipeline for Illumina HumanMethylation450 and EPIC

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The package includes quality control metrics, a selection of normalization methods and novel methods to identify differentially methylated regions and to highlight copy number alterations.

Author
Yuan Tian [cre,aut], Tiffany Morris [ctb], Lee Stirling [ctb], Andrew Feber [ctb], Andrew Teschendorff [ctb], Ankur Chakravarthy [ctb]
Date of publication
None
Maintainer
Yuan Tian <champ450k@gmail.com>
License
GPL-3
Version
2.4.0

View on Bioconductor

Man pages

Block.GUI
Generate interactive plot for the result of champ.Block()...
champ.Block
Identify Differential Methylation Blocks in Illumina...
champ.CNA
Inference of Copy Number Abberrations from intensity values.
champ.DMP
Identify Differential Methylation Positions (DMP) in Illumina...
champ.DMR
Applying Bumphunter, DMRcate or ProbeLasso Algorithms to...
champ.EpiMod
champ.EpiMod() infer differential methylation interactome...
champ.GSEA
Do GSEA for DMP, DMR and other methylation data related...
champ.impute
Conduct imputation for NA value on beta matrix and...
champ.load
Upload of raw HumanMethylation450K or HumanMethylationEPIC...
champ.norm
Normalization for HumanMethylation450 or HumanMethylationEPIC...
ChAMP-package
ChAMP-Chip Analysis Methylation Pipeline
champ.process
Process function to run all methods in ChAMP pipeline.
champ.QC
Plot quality control plot, mdsplot, densityPlot, dendrogram...
champ.refbase
Applying References-Base Methold to beta valued methylation...
champ.reffree
Applying RefFreeEWAS Methold to beta valued methylation data.
champ.runCombat
Function that uses ComBat to correct for batch effects....
champ.SVD
Singular Value Decomposition analysis for batch effects...
CpG.GUI
Generate interactive plot for summary information of a list...
DMP.GUI
Generate interactive plot for the result of champ.DMP()...
DMR.GUI
Generate interactive plot for the result of champ.DMR()...
QC.GUI
Generate interactive plot for Quality Control of a dataset

Files in this package

ChAMP/DESCRIPTION
ChAMP/NAMESPACE
ChAMP/R
ChAMP/R/Block.GUI.R
ChAMP/R/CheckBMIQ.R
ChAMP/R/CpG.GUI.R
ChAMP/R/DMP.GUI.R
ChAMP/R/DMR.GUI.R
ChAMP/R/DoPBC.R
ChAMP/R/EstDimRMTv2.R
ChAMP/R/QC.GUI.R
ChAMP/R/champ.BMIQ.R
ChAMP/R/champ.Block.R
ChAMP/R/champ.CNA.R
ChAMP/R/champ.ComBat.R
ChAMP/R/champ.DMP.R
ChAMP/R/champ.DMR.R
ChAMP/R/champ.EpiMod.R
ChAMP/R/champ.GSEA.R
ChAMP/R/champ.QC.R
ChAMP/R/champ.SVD.R
ChAMP/R/champ.colname.R
ChAMP/R/champ.impute.R
ChAMP/R/champ.load.R
ChAMP/R/champ.norm.R
ChAMP/R/champ.process.R
ChAMP/R/champ.read.R
ChAMP/R/champ.refbase.R
ChAMP/R/champ.reffree.R
ChAMP/R/champ.runCombat.R
ChAMP/R/zzz.R
ChAMP/build
ChAMP/build/vignette.rds
ChAMP/inst
ChAMP/inst/CITATION
ChAMP/inst/NEWS.Rd
ChAMP/inst/doc
ChAMP/inst/doc/ChAMP.R
ChAMP/inst/doc/ChAMP.Rmd
ChAMP/inst/doc/ChAMP.html
ChAMP/inst/extdata
ChAMP/inst/extdata/CNAimage.jpg
ChAMP/inst/extdata/CNAtext.jpg
ChAMP/inst/extdata/DMR.jpg
ChAMP/inst/extdata/DMRdistributionplot.png
ChAMP/inst/extdata/DMRoutput.jpg
ChAMP/inst/extdata/MVP1.jpg
ChAMP/inst/extdata/MVP2.jpg
ChAMP/inst/extdata/MVP3.jpg
ChAMP/inst/extdata/SVDsummary.pdf
ChAMP/inst/extdata/checkBMIQ.jpg
ChAMP/inst/extdata/densityPlot.jpg
ChAMP/inst/extdata/failedProbes.jpg
ChAMP/inst/extdata/figure1.pdf
ChAMP/inst/extdata/lasso.jpg
ChAMP/inst/extdata/logo4.jpg
ChAMP/inst/extdata/mdsPlot.jpg
ChAMP/inst/extdata/probeFeatures.jpg
ChAMP/inst/extdata/radius.jpg
ChAMP/inst/extdata/rawSampleCluster.jpg
ChAMP/inst/extdata/sampleSheetexample.jpg
ChAMP/inst/extdata/studyInfo.jpg
ChAMP/inst/extdata/studyInfo.png
ChAMP/inst/extdata/type1fit.jpg
ChAMP/inst/extdata/type2fit.jpg
ChAMP/man
ChAMP/man/Block.GUI.Rd
ChAMP/man/ChAMP-package.Rd
ChAMP/man/CpG.GUI.Rd
ChAMP/man/DMP.GUI.Rd
ChAMP/man/DMR.GUI.Rd
ChAMP/man/QC.GUI.Rd
ChAMP/man/champ.Block.Rd
ChAMP/man/champ.CNA.Rd
ChAMP/man/champ.DMP.Rd
ChAMP/man/champ.DMR.Rd
ChAMP/man/champ.EpiMod.Rd
ChAMP/man/champ.GSEA.Rd
ChAMP/man/champ.QC.Rd
ChAMP/man/champ.SVD.Rd
ChAMP/man/champ.impute.Rd
ChAMP/man/champ.load.Rd
ChAMP/man/champ.norm.Rd
ChAMP/man/champ.process.Rd
ChAMP/man/champ.refbase.Rd
ChAMP/man/champ.reffree.Rd
ChAMP/man/champ.runCombat.Rd
ChAMP/vignettes
ChAMP/vignettes/ChAMP.Rmd
ChAMP/vignettes/ChAMP.bib
ChAMP/vignettes/ChAMP.css
ChAMP/vignettes/Figure
ChAMP/vignettes/Figure/BMIQ.jpg
ChAMP/vignettes/Figure/Block-1.png
ChAMP/vignettes/Figure/Block-2.png
ChAMP/vignettes/Figure/Block-3.png
ChAMP/vignettes/Figure/CNA.jpg
ChAMP/vignettes/Figure/CNAGroupPlot.jpg
ChAMP/vignettes/Figure/ChAMP_Pipeline.png
ChAMP/vignettes/Figure/CpGGUI.png
ChAMP/vignettes/Figure/DMP-1.png
ChAMP/vignettes/Figure/DMP-2.png
ChAMP/vignettes/Figure/DMP-3.png
ChAMP/vignettes/Figure/DMP-4.png
ChAMP/vignettes/Figure/DMP-5.png
ChAMP/vignettes/Figure/DMR-1.png
ChAMP/vignettes/Figure/DMR-2.png
ChAMP/vignettes/Figure/DMR-3.png
ChAMP/vignettes/Figure/DMR-4.png
ChAMP/vignettes/Figure/EpiMod.jpg
ChAMP/vignettes/Figure/Logo.jpg
ChAMP/vignettes/Figure/MVP-1.png
ChAMP/vignettes/Figure/MVP-2.png
ChAMP/vignettes/Figure/MVP-3.png
ChAMP/vignettes/Figure/MVP-4.png
ChAMP/vignettes/Figure/MVP-5.png
ChAMP/vignettes/Figure/QCGUI.jpg
ChAMP/vignettes/academic-medicine.csl
ChAMP/vignettes/header.html