deviation.plot.beta: deviation.plot.beta

In RnBeads: RnBeads

Description

Creates a deviation plot based on the methylation beta values of a population.

Usage

deviation.plot.beta(betas, c.values = NULL, c.legend = NULL)

Arguments

betas	Non-empty numeric matrix of methylation beta values. Rows in this matrix must denote sites or regions, and columns - samples. If a locus (row in the matrix) contains missing values only, it is not included in the plot.
c.values	Vector (usually a factor) storing category or quantitative values for each site or region. The length of this vector must be equal to nrow(betas), the i-th element storing the property values for the i-th locus in betas. Note that this vector's names, if present, are ignored.
c.legend	If c.values stores categories, this parameter specifies the mapping from property values to colors. The mapping is in the form of a named character vector. All values that appear in c.values must be present among the names of this vector. The order of the values in this mapping determines in which order the colors are stacked (when the number of loci is large). If c.values denotes a quantitative measure, this parameter is a singleton integer, specifying the color scheme for visualizing the values. Currently, the only supported values are 2 and 3. See rnb.options for more details.

Value

Methylation variability as a number between 0 and 1, invisibly. This number denotes the relative area of variation in the generated plot.

Author(s)

Yassen Assenov

RnBeads documentation built on March 3, 2021, 2 a.m.