ChAMP: Chip Analysis Methylation Pipeline for Illumina HumanMethylation450 and EPIC

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.

AuthorYuan Tian [cre,aut], Tiffany Morris [ctb], Lee Stirling [ctb], Andrew Feber [ctb], Andrew Teschendorff [ctb], Ankur Chakravarthy [ctb]
Date of publicationNone
MaintainerYuan Tian <champ450k@gmail.com>
LicenseGPL-3
Version2.6.0

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.filter: Do filtering on beta or M matrix. So that user who have no...

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

Functions

Block.GUI Man page
ChAMP Man page
champ.Block Man page
champ.CNA Man page
champ.DMP Man page
champ.DMR Man page
champ.EpiMod Man page
champ.filter Man page
champ.GSEA Man page
champ.impute Man page
champ.load Man page
champ.norm Man page
ChAMP-package Man page
champ.process Man page
champ.QC Man page
champ.refbase Man page
champ.reffree Man page
champ.runCombat Man page
champ.SVD Man page
CpG.GUI Man page
DMP.GUI Man page
DMR.GUI Man page
QC.GUI Man page

Files

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.filter.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.filter.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

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

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

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