To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("ramwas")
In most cases, you don't need to download the package archive at all.
ramwas
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Fast Methylome-Wide Association Study Pipeline for Enrichment Platforms
Bioconductor version: Release (3.5)
RaMWAS provides a complete toolset for methylome-wide association studies (MWAS). It is specifically designed for data from enrichment based methylation assays, but can be applied to other data as well. The analysis pipeline includes seven steps: (1) scanning aligned reads from BAM files, (2) calculation of quality control measures, (3) creation of methylation score (coverage) matrix, (4) principal component analysis for capturing batch effects and detection of outliers, (5) association analysis with respect to phenotypes of interest while correcting for top PCs and known covariates, (6) annotation of significant findings, and (7) multi-marker analysis (methylation risk score) using elastic net. Additionally, RaMWAS include tools for joint analysis of methlyation and genotype data.
Author: Andrey A Shabalin [aut, cre], Shaunna L Clark [aut], Mohammad W Hattab [aut], Karolina A Aberg [aut], Edwin J C G van den Oord [aut]
Maintainer: Andrey A Shabalin <ashabalin at vcu.edu>
Citation (from within R,
enter citation("ramwas")):
Installation
To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("ramwas")
Documentation
| HTML | R Script | 1. Overview |
| HTML | R Script | 2. CpG sets |
| HTML | R Script | 3. BAM Quality Control Measures |
| HTML | R Script | 4. Joint Analysis of Methylation and Genotype Data |
| HTML | R Script | 5. Analyzing data from other sources |
| HTML | R Script | 6. RaMWAS parameters |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | BatchEffect, Coverage, DNAMethylation, DifferentialMethylation, Normalization, Preprocessing, PrincipalComponent, QualityControl, Sequencing, Software, Visualization |
| Version | 1.0.0 |
| In Bioconductor since | BioC 3.5 (R-3.4) (0.5 years) |
| License | LGPL-3 |
| Depends | R (>= 3.3.0), methods, filematrix |
| Imports | graphics, stats, utils, digest, glmnet, KernSmooth, grDevices, GenomicAlignments, Rsamtools, parallel, biomaRt, Biostrings, BiocGenerics |
| LinkingTo | |
| Suggests | knitr, rmarkdown, pander, BiocStyle, BSgenome.Hsapiens.UCSC.hg19, SNPlocs.Hsapiens.dbSNP144.GRCh37, BSgenome.Ecoli.NCBI.20080805 |
| SystemRequirements | |
| Enhances | |
| URL | https://bioconductor.org/packages/ramwas/ |
| BugReports | https://github.com/andreyshabalin/ramwas/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 | ramwas_1.0.0.tar.gz |
| Windows Binary | ramwas_1.0.0.zip (32- & 64-bit) |
| Mac OS X 10.11 (El Capitan) | ramwas_1.0.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/ramwas |
| Package Short Url | http://bioconductor.org/packages/ramwas/ |
| Package Downloads Report | Download Stats |
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