plotCpg: Plot methylation values at an single genomic position
In hansenlab/minfi: Analyze Illumina Infinium DNA methylation arrays

plotCpg

R Documentation

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.

Details

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

Value

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

Author(s)

Martin Aryee aryee@jhu.edu.

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")

}

hansenlab/minfi documentation built on May 3, 2024, 3:49 p.m.