missMethyl

Package: missMethyl
Type: Package
Title: Analysis of methylation array data
Version: 1.6.2
Date: 2016-02-16
Author: Belinda Phipson and Jovana Maksimovic
Maintainer: Belinda Phipson <belinda.phipson@mcri.edu.au>, Jovana
Maksimovic <jovana.maksimovic@mcri.edu.au>
Depends: R (>= 2.3.0)
Imports: limma, minfi, methylumi, IlluminaHumanMethylation450kmanifest,
statmod, ruv, stringr,
IlluminaHumanMethylation450kanno.ilmn12.hg19, org.Hs.eg.db,
AnnotationDbi, BiasedUrn
VignetteBuilder: knitr
Suggests: minfiData, BiocStyle, knitr, edgeR, tweeDEseqCountData
Description: Normalisation and testing for differential variability and
differential methylation for data from Illumina's Infinium
HumanMethylation450 array. The normalisation procedure is
subset-quantile within-array normalisation (SWAN), which allows
Infinium I and II type probes on a single array to be normalised
together. The test for differential variability is based on an
empirical Bayes version of Levene's test. Differential
methylation testing is performed using RUV, which can adjust for
systematic errors of unknown origin in high-dimensional data by
using negative control probes. Gene ontology analysis is performed
by taking into account the number of probes per gene on the
array.
License: GPL-2
biocViews: Normalization, DNAMethylation, MethylationArray,
GenomicVariation, GeneticVariability, DifferentialMethylation,
GeneSetEnrichment
NeedsCompilation: no
Packaged: 2016-05-16 04:44:16 UTC; biocbuild

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'missMethyl' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'missMethyl'
    finding HTML links ... done
    RUVadj                                  html  
    finding level-2 HTML links ... done

    RUVfit                                  html  
    SWAN                                    html  
    contrasts.varFit                        html  
    densityByProbeType                      html  
    getINCs                                 html  
    getLeveneResiduals                      html  
    getMappedEntrezIDs                      html  
    gometh                                  html  
    gsameth                                 html  
    missMethyl-package                      html  
    topGSA                                  html  
    topRUV                                  html  
    topVar                                  html  
    varFit                                  html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (missMethyl)
Making 'packages.html' ... done