UM_plot: U/M plot

In BenjaminPlanterose/UMtools: An R-package for analysing Illumina DNA Methylation arrays at the fluorescence intensity level

U/M plot

Description

Scatter plot of fluorescence intensities: unmethylated (U) fluorescence against methylated (M) fluorescence.

Usage

UM_plot(M, U, CpG, sex = NULL, xlim = NULL, ylim = NULL, alpha = 0.5)

Arguments

M	Methylated fluorescence mean intensity matrix (CpGs as rows, samples as columns)
U	Unmethylated fluorescence mean intensity matrix (CpGs as rows, samples as columns)
CpG	A CpG identifier (e.g. "cg15771735")
sex	vector of sex. First level is expected to be Female (coloured pink). Check levels(sex) to see if that is the case.
xlim	x-axis limit
ylim	y-axis limit
alpha	transparency

Details

More information on what it is referred as U/M fluorescence is available at help(GR_to_UM).

Value

Graphics

Examples

UM_plot(M = M, U = U, CpG = "cg00050873", sex = pheno$sex)

BenjaminPlanterose/UMtools documentation built on Aug. 19, 2024, 4:54 a.m.