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

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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.

Author
Martin Rijlaarsdam [aut, cre], Yvonne vd Zwan [aut], Lambert Dorssers [aut], Leendert Looijenga [aut]
Date of publication
None
Maintainer
Martin Rijlaarsdam <m.a.rijlaarsdam@gmail.com>
License
GPL (>= 2)
Version
1.10.0
URLs

View on Bioconductor

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

Files in this package

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