minfi (version 1.18.2)

plotCpg: Plot methylation values at an single genomic position

Description

Plot single-position (single CpG) methylation values as a function of a categorical or continuous phenotype

Usage

plotCpg(dat, cpg, pheno, type = c("categorical", "continuous"),
    measure = c("beta", "M"), ylim = NULL, ylab = NULL, xlab = "",
    fitLine = TRUE, mainPrefix = NULL, mainSuffix = NULL)

Arguments

dat

An RGChannelSet, a MethylSet or a matrix. We either use the getBeta (or getM for measure="M") function to get Beta values (or M-values) (for the first two) or we assume the matrix contains Beta values (or M-values).

cpg

A character vector of the CpG position identifiers to be plotted.

pheno

A vector of phenotype values.

type

Is the phenotype categorical or continuous?

measure

Should Beta values or log-ratios (M) be plotted?

ylim

y-axis limits.

ylab

y-axis label.

xlab

x-axis label.

fitLine

Fit a least-squares best fit line when using a continuous phenotype.

mainPrefix

Text to prepend to the CpG name in the plot main title.

mainSuffix

Text to append to the CpG name in the plot main title.

Value

• No return value. Plots are produced as a side-effect.

Details

This function plots methylation values (Betas or log-ratios) at individual CpG loci as a function of a phenotype.

Examples

if (require(minfiData)) {

grp <- pData(MsetEx)$Sample_Group
cpgs <- c("cg00050873", "cg00212031", "cg26684946", "cg00128718")
par(mfrow=c(2,2))
plotCpg(MsetEx, cpg=cpgs, pheno=grp, type="categorical")

}