MakeVolcano: Make volcano plots from the results of DE expression

In machalen/QualityGraphs: Make quality graphs for microarray data based on objects obtained witharoma affymetrix normalization.

Description

This function makes a volcano plot using the statistics in the matrix obtained with topTable() in limma. DE genes are coloured (positive or negative expressed) using p-value and logFC cut offs.

Usage

  MakeVolcano(TabDiff, adj=TRUE, p.cf, FC.cf, filePath, fileName)

Arguments

TabDiff	Matrix with the statistics obtained with limma and the function topTable()
adj	If TRUE adjusted p.Value in the TabDiff table is used
p.cf	P-value cut-off to colour the points in the scatterplot
FC.cf	LogFC cut-off to colour the points in the scatterplot
filePath	Output directory
fileName	Name of the output file

Details

This function makes a plot in png format using the results from the differential expression analysis with "limma" package. It uses the columns "adj.P.Val" or "P.Value" deppending on the value "adj" and the column logFC. Cut-off is used in order to indicate the DE genes in the scatterplot.

Value

The plot is created in the "filePath" directory with the name "fileName" in ".png" format.

Author(s)

Magdalena Arnal Segura <[e-mail]>.

machalen/QualityGraphs documentation built on Oct. 22, 2019, 8:29 p.m.