methyvim

DOI: 10.18129/B9.bioc.methyvim    

Targeted Variable Importance for Differential Methylation Analysis

Bioconductor version: Release (3.7)

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 and enter:

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

Documentation

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 1.2.0
License file LICENSE
Depends R (>= 3.4.0)
Imports stats, cluster, methods, ggplot2, ggsci, gridExtra, superheat, dplyr, gtools, tmle, future, doFuture, 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
Build Report  

Package Archives

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

Source Package methyvim_1.2.0.tar.gz
Windows Binary methyvim_1.2.0.zip
Mac OS X 10.11 (El Capitan) methyvim_1.2.0.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 http://bioconductor.org/packages/methyvim/
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