In yousefi138/dnamalci: Easy estimation of DNA methylation alcohol (DNAm-Alcs) scores

dnamalci

dnamalci is an R-package that provides functions to easily apply the DNA methylation alcohol scores (DNAm-Alcs) generated and characterized in :

Liu C, Marioni RE, Hedman ÅK, Pfeiffer L, Tsai P-C, Reynolds LM et al. A DNA methylation biomarker of alcohol consumption. Mol Psychiatry 2016. doi:10.1038/mp.2016.192.

Yousefi PD, Richmond R, Langdon R, Ness A, Liu C, Levy D et al. Validation and characterization of a DNA methylation alcohol biomarker across the life course. bioRxiv 2019. doi:10.1101/591404.

Installation

Only a few steps are needed to install dnamalci in R. Just run the following commands:

knitr::opts_chunk$set(
comment = ">",
error = FALSE,
tidy = FALSE,
echo = TRUE, 
warning = FALSE, 
message = FALSE,
width=85,
eval = TRUE)

install.packages("devtools") # if the devtools package is not installed
library(devtools)
install_github("yousefi138/dnamalci")

Example use

Load a DNA methylation beta matrix

First, load a matrix of DNA methylation beta values of your choosing.

dnamalci installs with a test dataset which is a subset of results from:

Tsaprouni LG, Yang T-P, Bell J, Dick KJ, Kanoni S, Nisbet J et al. Cigarette smoking reduces DNA methylation levels at multiple genomic loci but the effect is partially reversible upon cessation. Epigenetics 2014; 9: 1382–1396.

This dataset is publicly available at GEO accession number GSE50660 :

library(dnamalci)
betas <- dnamalci.load.test.data()

The only requirements of user supplied beta values for dnamalci are that they:

• be contained in a matrix-formatted object where rows are CpG sites and columns are samples
• rownames must contain CpG site names

head(rownames(betas))

View available DNAm-Alcs

List the 4 flavors of DNAm-Alcs from Liu et al. 2016 and Yousefi et al. 2019 that are available for implementation in dnamalci:

dnamalci.models()

Estimate the DNAm-Alc score from your target DNA methylation beta matrix

dnam.alc <- dnamalci(betas)
head(dnam.alc$score)

By default dnamalci() estimates the 144 CpG model from Liu et all, but all DNAm-Alcs can be estimated by specifying the model argument:

dnamalc.5cpg <- dnamalci(betas, model = "dnamalc.5cpg")

yousefi138/dnamalci documentation built on May 23, 2019, 2:01 a.m.