bott                    Example of sequencing data to test the
                        rankReads function.
calcSRmat               Calculation of the sorted rank matrix from the
                        dataset
calcSRmatMod            Calculation of the sorted rank matrix from the
                        dataset
cghData                 Example of aCGH "data file" for the fcros
                        package.
cghInfo                 Example of aCGH "info file" for the fcros
                        package.
chrMerge                Using a C code for merging chromosome segments
chrPlot                 Plot a chromosome data
chrPlot2                Plot a chromosome segmentation results
chrSegment              Segmentation of a chromosome data
dataSummary             Summarization of the detection results for a
                        list of chromosomes
fc2Calc                 Calculation of fold change using pairwise
                        comparison values
fcros                   Search for differentially expressed
                        genes/probes
fcros-package           A Method to Search for Differentially Expressed
                        Genes and to Detect Recurrent Chromosomal Copy
                        Number Aberrations
fcros2                  Search for differentially expressed
                        genes/probes
fcrosC                  Search for differentially expressed
                        genes/probes
fcrosFCmat              Calculation of a matrix of fold changes using
                        pairwise comparisons
fcrosMod                Search for differentially expressed genes or to
                        detect recurrent copy number aberration probes
fcrosRead               Read a tab delimited text file
fcrosTopN               Search for the top N changed genes or probes
fcrosTtest              Student t-test for detecting differentially
                        expressed genes
fcrosWrite              Writing the fcros() or pfco() results in a tab
                        delimited text file
fdata                   Example of dataset for the fcros package.
fvalTopN                Search for the top N changed genes or probes
                        using f-values
fvalVolcanoPlot         Performs a volcano plot of the FCROS/PFCO
                        statistics
histoPlot               Histogram plot function of the fcros package
                        results
moyStdCalc              Calculation of the mean and the standard
                        deviation of the full or reduced matrix of
                        sorted ranks
pfco                    Searching for differentially expressed
                        genes/probes using an approach based on the
                        Perron-Frobenius theorem
pfcoMod                 Searching for differentially expressed genes or
                        detecting recurrent copy number aberration
                        probes using an approach based on the
                        Perron-Frobenius theorem
pvalTopN                Search for the top N changed genes or probes
                        using p-values
pvalVolcanoPlot         Performs a volcano plot of the FCROS/PFCO
                        statistics
rankReads               This function computes a score to assess the
                        significance of sequencing values
rmatCalc                Calculation of the FC matrix using pairwise
                        comparisons
rmatTrim                Calculation of the reduced matrix containing
                        sorted rank values
scoreThr                Determine numerically a threshold for the
                        ranking score
tcnReads                Performs a total count normalization of reads
tprobaCalc              Calculation of the Student one sample test
                        probabilities
varBeta                 Compute variance of a beta distribution from
                        data
voomReads               Transformation of read count values
