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

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Documentation for package ‘fcros’ version 1.6.1

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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