DMRforPairs

Package: DMRforPairs
Version: 1.8.0
Date: 2014-03-03
Title: DMRforPairs: identifying Differentially Methylated Regions
between unique samples using array based methylation profiles
Authors@R: c(person("Martin", "Rijlaarsdam", role = c("aut", "cre"),
email = "m.a.rijlaarsdam@gmail.com"), person("Yvonne", "vd
Zwan", role = "aut"), person("Lambert", "Dorssers", role =
"aut"), person("Leendert", "Looijenga", role = "aut"))
Depends: R (>= 2.15.2), Gviz (>= 1.2.1), R2HTML (>= 2.2.1),
GenomicRanges (>= 1.10.7), parallel
Description: 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.
License: GPL (>= 2)
URL: http://www.martinrijlaarsdam.nl
http://www.erasmusmc.nl/pathologie/research/lepo/3898639/
biocViews: Microarray, DNAMethylation, DifferentialMethylation,
ReportWriting, Visualization, Annotation
Author: Martin Rijlaarsdam [aut, cre], Yvonne vd Zwan [aut], Lambert
Dorssers [aut], Leendert Looijenga [aut]
Maintainer: Martin Rijlaarsdam <m.a.rijlaarsdam@gmail.com>
NeedsCompilation: no
Packaged: 2016-05-04 05:25:22 UTC; biocbuild

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'DMRforPairs' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'DMRforPairs'
    finding HTML links ... done
    CL.methy                                html  
    DMRforPairs-package                     html  
    DMRforPairs                             html  
    calc_stats                              html  
    example_output_DMRforPairs              html  
    export_data                             html  
    merge_classes                           html  
    plot_annotate_custom_region             html  
    plot_annotate_gene                      html  
    plot_annotate_probes                    html  
    plot_annotate_region                    html  
    regionfinder                            html  
    testregion                              html  
    tune_parameters                         html  
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (DMRforPairs)
Making 'packages.html' ... done