plotMeanSD: Mean-Standard Deviation Plot

In LXQin/DANA: Data-driven Normalization Assessment for miRNA-Seq Data

Mean-Standard Deviation Plot

Description

Plots the marker-specific standard deviation over marker-specific means for log2-normalized read counts. Bounds for the definition of positive and negative controls can be highlighted by vertical lines (if given).

Usage

plotMeanSD(raw, tZero, tPoor, tWell, title, xlim.max = NA, ylim.max = NA)

Arguments

raw	Raw read count matrix (rows = genes, cols = samples).
tZero	Optional. Lower bound for negative controls.
tPoor	Optional. Upper bound for negative controls.
tWell	Optional. Lower bound for positive controls.
title	Plot title
xlim.max	Upper limit of the x-axis
ylim.max	Upper limit of the y-axis

Value

ggplot2 object of the mean-sd plot

Examples

counts <- matrix(rnbinom(1000, mu=3, size=0.01), nrow=50)
plotMeanSD(counts)

LXQin/DANA documentation built on March 7, 2024, 3:24 a.m.