methyvim

DOI: 10.18129/B9.bioc.methyvim    

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see methyvim.

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>

Installation

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

if (!requireNamespace("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")

 

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

Details

biocViews	Clustering, DNAMethylation, DifferentialMethylation, MethylSeq, MethylationArray, Software
Version	1.6.0
In Bioconductor since	BioC 3.6 (R-3.4) (2 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
LinkingTo
Suggests	testthat, knitr, rmarkdown, BiocStyle, SuperLearner, earth, nnet, gam, arm, snow, parallel, BatchJobs, minfiData, methyvimData
SystemRequirements
Enhances
URL	https://github.com/nhejazi/methyvim
BugReports	https://github.com/nhejazi/methyvim/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
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
Package Short Url	https://bioconductor.org/packages/methyvim/
Package Downloads Report	Download Stats