makeRLEplot: Create a Relative Log Expression (RLE) Plot

In gap: Genetic Analysis Package

Create a Relative Log Expression (RLE) Plot

Description

Generates a Relative Log Expression (RLE) plot for quality assessment of gene expression data. For each feature (row), the median expression across samples is subtracted, and boxplots of the resulting relative expression values are displayed for each sample.

Usage

makeRLEplot(
  E,
  log2.data = TRUE,
  groups = NULL,
  col.group = NULL,
  showTitle = FALSE,
  title = "Relative log expression (RLE) plot",
  ...
)

Arguments

E	A numeric matrix or data frame with features in rows and samples in columns.
log2.data	Logical; if TRUE, expression values are log2-transformed before computing RLE values.
groups	Optional factor or vector defining sample groups. Must have length equal to ncol(E).
col.group	Optional named vector of colours matching group levels.
showTitle	Logical; if TRUE, display a plot title.
title	Character string specifying the plot title.
...	Additional arguments passed to graphics::boxplot().

Value

Invisibly returns the matrix of relative log expression values.

Examples

## Not run: 
set.seed(123)
E <- matrix(rlnorm(987*200, meanlog=5, sdlog=1), nrow=987, ncol=200)
colnames(E) <- paste0("Sample_", seq_len(200))
rownames(E) <- paste0("Gene_", seq_len(987))
group <- rep(c("Control", "Treatment"), each=100)
col.group <- c(Control="steelblue", Treatment="tomato")
par(mar = c(10,4,4,2))
makeRLEplot(E,log2.data=TRUE,groups=group,col.group=col.group,cex=0.4,
  cex.axis=0.5,showTitle=TRUE,title="RLE plot (987 genes×200 samples)")

## End(Not run)

gap documentation built on Oct. 27, 2026, 1:07 a.m.