mvScatter {DMRMark}R Documentation

Visualize the distributions of M-value pairs from differentially methylated CpG sites (DMC) or non-DMCs

Description

Given the M-values, True DMCs and optional the experiment design, plot the scatter plot of M-values. DMCs are marked by red daggers and non-DMCs by green circles.

Usage

mvScatter(mv, isDMC, pd = NULL, nPlot = 5000)

Arguments

mv

The input M-values matrix, NA is not allowed.

isDMC

A binary vector corresponding to each row of 'mv'. 0 indicates non-DMC and 1 for DMC.

pd

A design matrix, which can be generated by 'stats::model.matrix'. If the M-values are totally paired or single paired, just leave it to be NULL.

nPlot

The maximum number of loci to be plotted. Using too large value will lead to messy scatter and long execution time. Default is 5000.

Value

This function only generates a figure and has no return value.

Author(s)

Linghao SHEN <sl013@ie.cuhk.edu.hk>

Examples


	# mvScatter
	data(BLCA)
	mvScatter(BLCA$mv, BLCA$truth, nPlot = 10000)

[Package DMRMark version 1.1.1 Index]