pvalTopN: Search for the top N changed genes or probes using p-values

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

Description

This function allows to seach for the top N differentially expressed genes or changed probes. It uses the p-value. These p-values can be obtained using one of the following functions fcros(), fcros2(), fcrosMod(), pfco(), pfcoMod() or another statistical method.

Usage

pvalTopN(pval, topN)

Arguments

pval	This is vector with p-values obtained using the functions fcros(), fcros2(), fcrosMod(), pfco(), pfcoMod() or another statistical method: pval = af$p.value
topN	The expected number of the top DE genes/probes in the dataset used: topN

Value

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

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);
   
   # now select top 10 down and/or up regulated genes
   top10 <- pvalTopN(af$p.value, 12);

   # display thresholds
   top10$alpha
   
   # display index of top10 genes
   fdata[top10$index, 1]
   
   # display fvalue of the top10 genes
   (af$f.value)[top10$index]

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