M3D: Identifies differentially methylated regions across testing groups

Share:

This package identifies statistically significantly differentially methylated regions of CpGs. It uses kernel methods (the Maximum Mean Discrepancy) to measure differences in methylation profiles, and relates these to inter-replicate changes, whilst accounting for variation in coverage profiles.

Author
Tom Mayo
Date of publication
None
Maintainer
Tom Mayo <t.mayo@ed.ac.uk>
License
Artistic License 2.0
Version
1.8.0

View on Bioconductor

Man pages

CpGsDemo
Toy data for the package - 1000 CpG regions to be tested in a...
determineGroupComps
Creates strings of sample pair comparisons
findComps
Finds columns in the M3D test-statistic matrix
M3D-package
Non-parametric statistical testing
M3D_Para
Computes the components of the M3D test-statistic over all...
M3D_Para_lite
Computes the components of the M3D test-statistic over all...
M3D_Single
Computes the components of the M3D test-statistic over one...
M3D_Wrapper
Computes the components of the M3D test-statistic over all...
M3D_Wrapper_lite
Computes the components of the M3D test-statistic over all...
median_freq
Finds the median
medianFreq
Finds the median
MMDlistDemo
Toy data for the package - the output of the M3D_Wrapper...
PDemo
Toy data for the package - the output of the pvals function.
plotCoverageSampleProfiles
Plots coverage profiles over a specific region
plotMethProfile
Plots methylation profiles over a specific region
plotMethSampleProfiles
Plots methylation profiles over a specific region
pvals
Computes p-values
pvals_lite
Computes p-values
readBedFiles
Reads in bed file to make RRBS data
readBedRaw
Reads in RRBS data in raw format to be processed later
rrbsDemo
Toy data for the package - methylation data for cytosines...
test_colData_structure
Tests that the files are specified in a workable order for...

Files in this package

M3D/.BBSoptions
M3D/DESCRIPTION
M3D/NAMESPACE
M3D/NEWS
M3D/R
M3D/R/M3D.R
M3D/R/M3D_Para.R
M3D/R/M3D_Para_lite.R
M3D/R/M3D_Single.R
M3D/R/M3D_Wrapper.R
M3D/R/M3D_Wrapper_lite.R
M3D/R/RcppExports.R
M3D/R/determineGroupComps.R
M3D/R/findComps.R
M3D/R/medianFreq.R
M3D/R/plotCoverageSampleProfiles.R
M3D/R/plotMethProfile.R
M3D/R/plotMethSampleProfiles.R
M3D/R/pvals.R
M3D/R/pvals_lite.R
M3D/R/readBedFiles.R
M3D/R/readBedRaw.R
M3D/R/test_colData_structure.R
M3D/build
M3D/build/vignette.rds
M3D/data
M3D/data/CpGsDemo.rda
M3D/data/MMDlistDemo.rda
M3D/data/PDemo.rda
M3D/data/datalist
M3D/data/rrbsDemo.rda
M3D/inst
M3D/inst/doc
M3D/inst/doc/M3D_vignette.R
M3D/inst/doc/M3D_vignette.Rnw
M3D/inst/doc/M3D_vignette.pdf
M3D/man
M3D/man/CpGsDemo.Rd
M3D/man/M3D-package.Rd
M3D/man/M3D_Para.Rd
M3D/man/M3D_Para_lite.Rd
M3D/man/M3D_Single.Rd
M3D/man/M3D_Wrapper.Rd
M3D/man/M3D_Wrapper_lite.Rd
M3D/man/MMDlistDemo.Rd
M3D/man/PDemo.Rd
M3D/man/determineGroupComps.Rd
M3D/man/findComps.Rd
M3D/man/medianFreq.Rd
M3D/man/median_freq.Rd
M3D/man/plotCoverageSampleProfiles.Rd
M3D/man/plotMethProfile.Rd
M3D/man/plotMethSampleProfiles.Rd
M3D/man/pvals.Rd
M3D/man/pvals_lite.Rd
M3D/man/readBedFiles.Rd
M3D/man/readBedRaw.Rd
M3D/man/rrbsDemo.Rd
M3D/man/test_colData_structure.Rd
M3D/src
M3D/src/RcppExports.cpp
M3D/src/cpp_fns.cpp
M3D/tests
M3D/tests/testthat
M3D/tests/testthat.R
M3D/tests/testthat/test_hidden_fns.R
M3D/tests/testthat/test_lite_fns.R
M3D/tests/testthat/test_non_lite_fns.R
M3D/vignettes
M3D/vignettes/M3D_vignette-M3DhistPlot.pdf
M3D/vignettes/M3D_vignette-M3DstatPlot.pdf
M3D/vignettes/M3D_vignette.Rnw
M3D/vignettes/M3D_vignette.bib