methyvim

This package is for version 3.9 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see methyvimData.

Targeted, Robust, and Model-free Differential Methylation Analysis


Bioconductor version: 3.9

This package provides facilities for differential methylation analysis based on variable importance measures (VIMs), a class of statistical target parameters that arise in causal inference. The estimation and inference procedures provided are nonparametric, relying on ensemble machine learning to flexibly assess functional relationships among covariates and the outcome of interest. These tools can be applied to differential methylation at the level of CpG sites, to obtain valid statistical inference even after corrections for multiple hypothesis testing.

Author: Nima Hejazi [aut, cre, cph], Mark van der Laan [aut, ths], Alan Hubbard [ctb, ths], Rachael Phillips [ctb]

Maintainer: Nima Hejazi <nhejazi at berkeley.edu>

Citation (from within R, enter citation("methyvim")):

Installation

To install this package, start R (version "3.6") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("methyvim")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("methyvim")
Targeted Data-Adaptive Estimation and Inference for Differential Methylation Analysis HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews Clustering, DNAMethylation, DifferentialMethylation, MethylSeq, MethylationArray, Software
Version 1.6.0
In Bioconductor since BioC 3.6 (R-3.4) (6.5 years)
License file LICENSE
Depends R (>= 3.4.0)
Imports stats, cluster, methods, ggplot2, ggsci, gridExtra, superheat, dplyr, gtools, tmle, future, doFuture, S4Vectors, BiocGenerics, BiocParallel, SummarizedExperiment, GenomeInfoDb, bumphunter, IRanges, limma, minfi
System Requirements
URL https://github.com/nhejazi/methyvim
Bug Reports https://github.com/nhejazi/methyvim/issues
See More
Suggests testthat, knitr, rmarkdown, BiocStyle, SuperLearner, earth, nnet, gam, arm, snow, parallel, BatchJobs, minfiData, methyvimData
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
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Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package methyvim_1.6.0.tar.gz
Windows Binary methyvim_1.6.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) methyvim_1.6.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/methyvim
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/methyvim
Bioc Package Browser https://code.bioconductor.org/browse/methyvim/
Package Short Url https://bioconductor.org/packages/methyvim/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.9 Source Archive