missMethyl: Analysing Illumina HumanMethylation BeadChip Data

Normalisation and testing for differential variability and differential methylation for data from Illumina's Infinium HumanMethylation450 array. The normalisation procedure is subset-quantile within-array normalisation (SWAN), which allows Infinium I and II type probes on a single array to be normalised together. The test for differential variability is based on an empirical Bayes version of Levene's test. Differential methylation testing is performed using RUV, which can adjust for systematic errors of unknown origin in high-dimensional data by using negative control probes. Gene ontology analysis is performed by taking into account the number of probes per gene on the array.

Author
Belinda Phipson and Jovana Maksimovic
Date of publication
None
Maintainer
Belinda Phipson <belinda.phipson@mcri.edu.au>, Jovana Maksimovic <jovana.maksimovic@mcri.edu.au>
License
GPL-2
Version
1.8.0

View on Bioconductor

Man pages

contrasts.varFit
Compute contrasts for a varFit object.
densityByProbeType
Plot the beta value distributions of the Infinium I and II...
getINCs
Extract intensity data for 613 Illumina negative controls...
getLeveneResiduals
Obtain Levene residuals
getMappedEntrezIDs
Get mapped Entrez Gene IDs from CpG probe names
gometh
Gene ontology testing for Ilumina methylation array data
gsameth
Generalised gene set testing for Illumina's methylation array...
missMethyl-package
Introduction to the missMethyl package
RUVadj
Adjust estimated variances
RUVfit
Remove unwanted variation when testing for differential...
SWAN
Subset-quantile Within Array Normalisation for Illumina...
topGSA
Get table of top 20 enriched pathways
topRUV
Table of top-ranked differentially methylated CpGs obatained...
topVar
Table of top-ranked differentially variable CpGs
varFit
Testing for differential variability

Files in this package

missMethyl/DESCRIPTION
missMethyl/NAMESPACE
missMethyl/R
missMethyl/R/DiffVar.R
missMethyl/R/RUVfunctions.R
missMethyl/R/SWAN.R
missMethyl/R/gometh.R
missMethyl/R/gsameth.R
missMethyl/R/plottingFunctions.R
missMethyl/build
missMethyl/build/vignette.rds
missMethyl/inst
missMethyl/inst/CITATION
missMethyl/inst/NEWS.Rd
missMethyl/inst/doc
missMethyl/inst/doc/missMethyl.R
missMethyl/inst/doc/missMethyl.Rmd
missMethyl/inst/doc/missMethyl.html
missMethyl/man
missMethyl/man/RUVadj.Rd
missMethyl/man/RUVfit.Rd
missMethyl/man/SWAN.Rd
missMethyl/man/contrasts.varFit.Rd
missMethyl/man/densityByProbeType.Rd
missMethyl/man/getINCs.Rd
missMethyl/man/getLeveneResiduals.Rd
missMethyl/man/getMappedEntrezIDs.Rd
missMethyl/man/gometh.Rd
missMethyl/man/gsameth.Rd
missMethyl/man/missMethyl-package.Rd
missMethyl/man/topGSA.Rd
missMethyl/man/topRUV.Rd
missMethyl/man/topVar.Rd
missMethyl/man/varFit.Rd
missMethyl/vignettes
missMethyl/vignettes/bibliography.bib
missMethyl/vignettes/missMethyl.Rmd