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

Documentation for package ‘fcros’ version 1.4.1

fcros-package	A Method to Search for Differentially Expressed Genes and to Detect Recurrent Chromosomal Copy Number Aberrations
cghData	Example of aCGH "data file" for the fcros package.
cghInfo	Example of aCGH "info file" for the fcros package.
fcros	fcros() to search for differentially expressed genes/probes
fcros2	fcros2() to search for differentially expressed genes/probes
fcrosC	fcros() to search for differentially expressed genes/probes
fcrosChrMerge	Using a C code for merging
fcrosChrPlot	Plot a chromosome data
fcrosChrPlot2	Plot a chromosome segmentation results
fcrosChrSegment	Segmentation of a chromosome data
fcrosChrSegmentC	Segmentation of a chromosome data
fcrosChrSummary	Summarization of the detection results for a list of chromosomes
fcrosFCmat	fcrosFCmat(): Computation of a matrix of change values
fcrosHistoPlot	fcrosHistoPlot(): Histogram plot function of the fcros results
fcrosMod	fcrosMod() to search for differentially expressed genes or to detect recurrent copy number aberration probes
fcrosRead	fcrosRead(): for reading a tab delimited text file
fcrosTopN	fcrosTopN(): Search for the top N changed genes/probes
fcrosTtest	Student t-test for detecting differentially expressed genes
fcrosVolcanoPlot	fcrosVolcanoPlot(): Performs a volcano plot of the fcros statistics
fcrosWrite	fcrosWrite(): to write the fcros results in file
fdata	Example of dataset for the fcros package.
rmatCalc	Using a C code for calculatin the pairwise matrix of FC