DMRforPairs: DMRforPairs: identifying Differentially Methylated Regions between unique samples using array based methylation profiles
Version 1.12.0

DMRforPairs (formerly DMR2+) allows researchers to compare n>=2 unique samples with regard to their methylation profile. The (pairwise) comparison of n unique single samples distinguishes DMRforPairs from other existing pipelines as these often compare groups of samples in either single CpG locus or region based analysis. DMRforPairs defines regions of interest as genomic ranges with sufficient probes located in close proximity to each other. Probes in one region are optionally annotated to the same functional class(es). Differential methylation is evaluated by comparing the methylation values within each region between individual samples and (if the difference is sufficiently large), testing this difference formally for statistical significance.

Browse man pages Browse package API and functions Browse package files

AuthorMartin Rijlaarsdam [aut, cre], Yvonne vd Zwan [aut], Lambert Dorssers [aut], Leendert Looijenga [aut]
Bioconductor views Annotation DNAMethylation DifferentialMethylation Microarray ReportWriting Visualization
Date of publicationNone
MaintainerMartin Rijlaarsdam <m.a.rijlaarsdam@gmail.com>
LicenseGPL (>= 2)
Version1.12.0
URL http://www.martinrijlaarsdam.nl http://www.erasmusmc.nl/pathologie/research/lepo/3898639/
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("DMRforPairs")

Man pages

calc_stats: CALCULATE DESCRIPTIVE AND TEST STATISTICS
CL.methy: METHYLATION DATA OF 4 CELL LINES (CHR 7)
DMRforPairs: WRAPPER FOR THE DMRforPairs ANALSYSIS
DMRforPairs-package: DMRforPairs package
example_output_DMRforPairs: EXAMPLE OF DMRforPairs RESULTS
export_data: COMPLETE EXPORT AND VISUALIZATION OF DMRforPairs RESULTS
merge_classes: MERGE ILLUMINA PROBE CLASSES
plot_annotate_custom_region: PLOT METHYLATION OF A CUSTOM GENOMIC REGION
plot_annotate_gene: PLOT METHYLATION VALUES AROUND A GENE
plot_annotate_probes: PLOT METHYLATION+ANNOTATE A SET OF PROBES
plot_annotate_region: PLOT METHYLATION AND ANNOTATE REGION
regionfinder: IDENTIFICATION OF PROBE DENSE REGIONS
testregion: METHYLATION DIFFERENECE & TESTING FOR 1 REGIONID
tune_parameters: TUNE MIN_DISTANCE AND MIN_N PARAMETERS

Functions

CL.methy Man page
DMRforPairs Man page Source code
DMRforPairs-package Man page
calc_stats Man page Source code
example_output_DMRforPairs Man page
export_data Man page Source code
matchsymbol Source code
merge_classes Man page Source code
mod Source code
plot_annotate_custom_region Man page Source code
plot_annotate_gene Man page Source code
plot_annotate_probes Man page Source code
plot_annotate_region Man page Source code
regionfinder Man page Source code
testregion Man page Source code
tune_parameters Man page Source code
tune_parameters_calc Source code

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/functions.R
build
build/vignette.rds
data
data/DMRforPairs_data.RData
data/datalist
inst
inst/CITATION
inst/doc
inst/doc/DMRforPairs_vignette.R
inst/doc/DMRforPairs_vignette.Rnw
inst/doc/DMRforPairs_vignette.pdf
man
man/CL.methy.Rd
man/DMRforPairs-package.Rd
man/DMRforPairs.Rd
man/calc_stats.Rd
man/example_output_DMRforPairs.Rd
man/export_data.Rd
man/figures
man/figures/FunctionSchedule.png
man/merge_classes.Rd
man/plot_annotate_custom_region.Rd
man/plot_annotate_gene.Rd
man/plot_annotate_probes.Rd
man/plot_annotate_region.Rd
man/regionfinder.Rd
man/testregion.Rd
man/tune_parameters.Rd
vignettes
vignettes/16.png
vignettes/16_annotated.png
vignettes/BMPER.png
vignettes/BMPER_TSS.png
vignettes/BMPER_TSS_annotated.png
vignettes/BMPER_annotated.png
vignettes/DMRforPairs_vignette.Rnw
vignettes/FunctionSchedule.png
vignettes/OutputTable.png
vignettes/PIK3CG.png
vignettes/PIK3CG_annotated.png
DMRforPairs documentation built on May 20, 2017, 9:15 p.m.