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 Feb. 4, 2023, 5 a.m.