fcrosTopN {fcros}

Search for the top N changed genes or probes

Description

This function allows to seach for the top N differentially expressed genes or changed probes. It uses the output results obtained using one of the following functions fcros(), fcros2(), fcrosMod(), pfco() or pfcoMod().

Usage

fcrosTopN(af, topN)

Arguments

af

This is an output object obtained using the functions fcros(), fcros2(), fcrosMod(), pfco() or pfcoMod().

topN

The expected number of the top DE genes in the dataset used.

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

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 <- fcrosTopN(af, 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]