limma_trend_plot: Mean-variance trend plot

In jdreyf/jdcbioinfo: Joslin Diabetes Center bioinformatics utilities

Mean-variance trend plot

Description

Estimate the mean-variance relationship and plot its trend using limma and ggplot2.

Usage

limma_trend_plot(
  object,
  design = NULL,
  name = NA,
  span = 0.5,
  alpha = 0.5,
  width = 7,
  height = 7,
  ...
)

Arguments

object	A matrix-like data object containing log-ratios or log-expression values for a series of arrays, with rows corresponding to genes and columns to samples. Any type of data object that can be processed by getEAWP is acceptable.
design	the design matrix of the microarray experiment, with rows corresponding to samples and columns to coefficients to be estimated. Defaults to object$design if that is non-NULL, otherwise to the unit vector meaning that all samples will be treated as replicates of a single treatment group.
name	file name for plot
span	width of the smoothing window used for the lowess mean-variance trend. Expressed as a proportion between 0 and 1.
alpha	Transparency, passed to geom_point.
width, height	the width and height of the graphics region in inches. The default values are 7.
...	Passed to lmFit.

jdreyf/jdcbioinfo documentation built on April 15, 2024, 6:37 p.m.