DESCRIPTION

Package: coMethDMR
Title: Accurate identification of co-methylated and differentially methylated
  regions in epigenome-wide association studies
Version: 0.99.18
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://gabrielodom.github.io/coMethDMR/