fvalVolcanoPlot {fcros} | R Documentation |
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().
fvalVolcanoPlot(af, thr = 0.05)
af |
This is an object obtained using the functions fcros(),
fcros2(), fcrosMod(), pfco() or pfcoMod():
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thr |
The threshold to obtain the DE genes in the dataset (red plots):
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This function displays on the screen a volcano like plot using the f-values and the robust fold changes (FC2).
Doulaye Dembele doulaye@igbmc.fr
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
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);