MAplot: MA plot

In amberjoybarton/sweetD: Hoeffding's D Statistic as a Summary Statistic for MA Plots

Description

This function allows you to take a log-transformed expression matrix, and specify one (in which case it will be compared to the median) or two samples, outputing an MA plot, where A = mean expression count or intensity and M = log fold difference

Usage

MAplot(expression, sample1, sample2 = NULL)

Arguments

expression	A log-transformed expression matrix, with columns corresponding to samples and rows to genes or other features.
sample1	Character string specifiying the name of a column in your expression matrix, corresponding to a sample
sample2	Character string specifiying the name of a column in your expression matrix, corresponding to a sample. Defaults to the median if not specified.

Examples

data(expr.raw, expr.batchcorrected, expr.normalised)
MAplot(expr.raw, "S8")
MAplot(expr.raw, "S8", "S15")
MAplot(expr.normalised, "S8", "S15")

amberjoybarton/sweetD documentation built on Feb. 27, 2021, 3:44 a.m.