fvalTopN {fcros} | R Documentation |
This function allows to seach for the top N differentially expressed genes or changed probes. It uses the f-values obtained using one of the following functions fcros(), fcros2(), fcrosMod(), pfco() or pfcoMod().
fvalTopN(fval, topN)
fval |
This is a f-values vector obtained using the functions fcros(),
fcros2(), fcrosMod(), pfco() or pfcoMod(): |
topN |
The expected number of the top DE genes/probes in the dataset used. |
This function returns a data frame containing 2 components
alpha |
Two threshold values for the down- and the up-regulated allowing to have the top N DE genes |
index |
The indexes of the top N DE genes / probes |
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 pfco() af <- pfco(fdata, cont, test, log2.opt); # now select top 10 down and/or up regulated genes top10 <- fvalTopN(af$f.value, 10); # display thresholds top10$alpha # display index of top10 genes fdata[top10$index, 1] # display fvalue of the top10 genes (af$f.value)[top10$index]