methyvim

DOI: 10.18129/B9.bioc.methyvim    

Differential Methylation Analysis with Targeted Minimum Loss-Based Estimates of Variable Importance Measures

Bioconductor version: Release (3.6)

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 relationship among covariates and the outcome of interest. These tools can be applied to differential methylation at the level of CpG sites, with valid inference after multiple hypothesis testing.

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

Maintainer: Nima Hejazi <nhejazi at berkeley.edu>

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("methyvim")

Documentation

HTML	R Script	methyvim: Variable Importance for DNA Methylation
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	Clustering, DNAMethylation, DifferentialMethylation, MethylSeq, MethylationArray, Software
Version	1.0.0
License	file LICENSE
Depends	R (>= 3.4.0)
Imports	stats, cluster, methods, ggplot2, gridExtra, superheat, wesanderson, magrittr, dplyr, gtools, tmle, future, doFuture, BiocParallel, BiocGenerics, 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
Build Report

Package Archives

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

Source Package	methyvim_1.0.0.tar.gz
Windows Binary	methyvim_1.0.0.zip
Mac OS X 10.11 (El Capitan)	methyvim_1.0.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/methyvim
Package Short Url	http://bioconductor.org/packages/methyvim/
Package Downloads Report	Download Stats