Package: ramwas
Type: Package
Title: Fast Methylome-Wide Association Study Pipeline for Enrichment
        Platforms
Version: 1.2.0
Date: 2017-03-20
Authors@R: c(person("Andrey A", "Shabalin",
                    role = c("aut", "cre"),
                    email = "ashabalin@vcu.edu"),
            person("Shaunna L", "Clark",
                    email = "slclark2@vcu.edu",
                    role = "aut"),
            person("Mohammad W", "Hattab",
                    email = "mwhattab@vcu.edu",
                    role = "aut"),
            person("Karolina A", "Aberg",
                    email = "kaaberg@vcu.edu",
                    role = "aut"),
            person("Edwin J C G", "van den Oord",
                    email = "ejvandenoord@vcu.edu",
                    role = "aut"))
Maintainer: Andrey A Shabalin <ashabalin@vcu.edu>
Description: RaMWAS provides a complete toolset for 
    methylome-wide association studies (MWAS).
    It is specifically designed for data from 
    enrichment based methylation assays,
    but can be applied to other data as well.
    The analysis pipeline includes seven steps:
    (1) scanning aligned reads from BAM files,
    (2) calculation of quality control measures,
    (3) creation of methylation score (coverage) matrix,
    (4) principal component analysis for capturing batch effects and
    detection of outliers,
    (5) association analysis with respect to phenotypes of interest
    while correcting for top PCs and known covariates,
    (6) annotation of significant findings, and
    (7) multi-marker analysis (methylation risk score) using elastic net.
    Additionally, RaMWAS include tools for joint analysis of methlyation and
    genotype data.
URL: https://bioconductor.org/packages/ramwas/
BugReports: https://github.com/andreyshabalin/ramwas/issues
License: LGPL-3
LazyLoad: yes
NeedsCompilation: yes
Depends: R (>= 3.3.0), methods, filematrix
VignetteBuilder: knitr
Suggests: knitr, rmarkdown, pander, BiocStyle,
        BSgenome.Hsapiens.UCSC.hg19, SNPlocs.Hsapiens.dbSNP144.GRCh37,
        BSgenome.Ecoli.NCBI.20080805
Imports: graphics, stats, utils, digest, glmnet, KernSmooth, grDevices,
        GenomicAlignments, Rsamtools, parallel, biomaRt, Biostrings,
        BiocGenerics
biocViews: DNAMethylation, Sequencing, QualityControl, Coverage,
        Preprocessing, Normalization, BatchEffect, PrincipalComponent,
        DifferentialMethylation, Visualization
Packaged: 2017-10-31 02:02:42 UTC; biocbuild
Author: Andrey A Shabalin [aut, cre],
  Shaunna L Clark [aut],
  Mohammad W Hattab [aut],
  Karolina A Aberg [aut],
  Edwin J C G van den Oord [aut]
Built: R 3.4.2; i386-w64-mingw32; 2017-10-31 07:22:19 UTC; windows
Archs: i386, x64
