plot_glimma: plot_glimma

In askomics/askoR: askoR - Differential Expresion Analysis using edgeR

plot_glimma

Description

Use Glimma package for interactive visualization of results from differential expression analyses. Two types of graphs can be created:

• Mean-Difference Plot of Expression Data (aka MA plot).

• Volcano plot for a specified coefficient/contrast of a linear model.

Usage

plot_glimma(fit, normGE, resDE, contrast, tplot, parameters)

Arguments

fit	fitted linear model object.
normGE	large DGEList with normalized counts and data description.
resDE	vector containing integer values of -1 to represent down-regulated genes, 0 for no differential expression, and 1 for up-regulated genes.
contrast	coefficient/contrast tested.
tplot	type of plot selected for display.
parameters	list that contains all arguments charged in Asko_start.

Value

none.

Examples

## Not run: 
   plot_glimma(fit, normGE, resDE, contrast, "MD", parameters)  # smear plot
   plot_glimma(fit, normGE, resDE, contrast, "VO", parameters)  # volcano plot

## End(Not run)

askomics/askoR documentation built on Aug. 11, 2024, 11:05 p.m.