fvalVolcanoPlot: Performs a volcano plot of the FCROS/PFCO statistics

In fcros: A Method to Search for Differentially Expressed Genes and to Detect Recurrent Chromosomal Copy Number Aberrations

Description

This function allows to have a volcano like plot using the output results of the function fcros(), fcros2(), fcrosMod(), pfco() or pfcoMod(): p-values versus robust fold changes (FC2). The p-value are transformed using -log10(), while FC2 are transformed using log2().

Usage

fvalVolcanoPlot(af, thr = 0.05)

Arguments

af	This is an object obtained using the functions fcros(), fcros2(), fcrosMod(), pfco() or pfcoMod(): af = fcros(xdata, cont, test)
thr	The threshold to obtain the DE genes in the dataset (red plots): thr = 0.05

Value

This function displays on the screen a volcano like plot using the f-values and the robust fold changes (FC2).

Author(s)

Doulaye Dembele [e-mail]

References

Dembele D and Kastner P, Fold change rank ordering statistics: a new method for detecting differentially expressed genes, BMC bioinformatics, 2014, 15:14

Dembele D and Kastner P, Comment on: Fold change rank ordering statistics: a new method for detecting differentially expressed genes, BMC Bioinformatics, 2016, 17:462

Examples

   data(fdata);
   rownames(fdata) <- fdata[,1];

   cont <- c("cont01", "cont07", "cont03", "cont04", "cont08");
   test <- c("test01", "test02", "test08", "test09", "test05");
   log2.opt <- 0;

   # perform fcros()
   af <- fcros(fdata, cont, test, log2.opt);
   
   # Volcano plot
   fvalVolcanoPlot(af, thr = 0.01);

fcros documentation built on May 31, 2019, 5:03 p.m.