# A Method to Search for Differentially Expressed Genes and to Detect Recurrent Chromosomal Copy Number Aberrations

## Documentation for package ‘fcros’ version 1.6.1

- DESCRIPTION file.

## Help Pages

fcros-package | A Method to Search for Differentially Expressed Genes and to Detect Recurrent Chromosomal Copy Number Aberrations
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
fcros2 | 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