Package: coMethDMR
Title: Accurate identification of co-methylated and differentially
        methylated regions in epigenome-wide association studies
Version: 1.0.0
Authors@R: c(
  person("Fernanda", "Veitzman", email = "fveit001@fiu.edu", role = c("cre")),
  person("Lissette", "Gomez", email = "lxg255@miami.edu", role = c("aut")),
  person("Tiago", "Silva", email = "txs902@med.miami.edu", role = c("aut")),
  person("Ning", "Lijiao", role = c("ctb")),
  person("Boissel", "Mathilde", role = c("ctb")),
  person("Lily", "Wang", email = "lily.wang@med.miami.edu", role = c("aut")),
  person("Gabriel", "Odom", email = "gabriel.odom@fiu.edu", role = c("aut"))
  )
Description: coMethDMR identifies genomic regions associated with continuous
  phenotypes by optimally leverages covariations among CpGs within predefined
  genomic regions. Instead of testing all CpGs within a genomic region,
  coMethDMR carries out an additional step that selects co-methylated
  sub-regions first without using any outcome information. Next, coMethDMR tests
  association between methylation within the sub-region and continuous phenotype
  using a random coefficient mixed effects model, which models both variations
  between CpG sites within the region and differential methylation
  simultaneously. 
Depends: R (>= 4.1)
License: GPL-3
Encoding: UTF-8
LazyData: false
RoxygenNote: 7.1.2
Imports: AnnotationHub, BiocParallel, bumphunter, ExperimentHub,
        GenomicRanges, IRanges, lmerTest, methods, stats, utils
Suggests: BiocStyle, corrplot, knitr, rmarkdown, testthat,
        IlluminaHumanMethylation450kanno.ilmn12.hg19,
        IlluminaHumanMethylationEPICanno.ilm10b4.hg19
biocViews: DNAMethylation, Epigenetics, MethylationArray,
        DifferentialMethylation, GenomeWideAssociation
VignetteBuilder: knitr
BugReports: https://github.com/TransBioInfoLab/coMethDMR/issues
URL: https://github.com/TransBioInfoLab/coMethDMR
git_url: https://git.bioconductor.org/packages/coMethDMR
git_branch: RELEASE_3_15
git_last_commit: 1f363f7
git_last_commit_date: 2022-04-26
Date/Publication: 2022-04-26
NeedsCompilation: no
Packaged: 2022-04-26 22:09:04 UTC; biocbuild
Author: Fernanda Veitzman [cre],
  Lissette Gomez [aut],
  Tiago Silva [aut],
  Ning Lijiao [ctb],
  Boissel Mathilde [ctb],
  Lily Wang [aut],
  Gabriel Odom [aut]
Maintainer: Fernanda Veitzman <fveit001@fiu.edu>
Built: R 4.2.0; ; 2022-04-27 09:20:00 UTC; windows
