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

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A fold change rank based method is presented to search for differentially expressed genes and to detect recurrent chromosomal copy number aberrations. This method may be useful for high-throughput biological data (microarray, sequencing, ...). Probabilities are associated with genes/probes in the dataset and there is no problem of multiple tests when using this method. For aCGH data, segmentation results are obtained by merging the significant probes detected.

Author
Doulaye Dembele
Date of publication
2016-11-17 08:27:34
Maintainer
Doulaye Dembele <doulaye@igbmc.fr>
License
GPL (>= 2)
Version
1.5.2

View on CRAN

Man pages

cghData
Example of aCGH "data file" for the fcros package.
cghInfo
Example of aCGH "info file" for the fcros package.
fcros
Search for differentially expressed genes/probes
fcros2
Search for differentially expressed genes/probes
fcrosC
Search for differentially expressed genes/probes
fcrosFCmat
Calculation of a matrix of fold changes using pairwise...
fcrosMod
Search for differentially expressed genes or to detect...
fcros-package
A Method to Search for Differentially Expressed Genes and to...
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...
fdata
Example of dataset for the fcros package.

Files in this package

fcros
fcros/src
fcros/src/fcros.cpp
fcros/NAMESPACE
fcros/data
fcros/data/cghInfo.rda
fcros/data/cghData.rda
fcros/data/datalist
fcros/data/fdata.rda
fcros/R
fcros/R/pfco.R
fcros/R/moyStdCalc.R
fcros/R/tprobaCalc.R
fcros/R/fcros2.R
fcros/R/fcros.R
fcros/R/fcrosWrite.R
fcros/R/voomReads.R
fcros/R/histoPlot.R
fcros/R/dataSummary.R
fcros/R/chrPlot.R
fcros/R/fcrosMod.R
fcros/R/pvalVolcanoPlot.R
fcros/R/fcrosTtest.R
fcros/R/fcrosRead.R
fcros/R/fcrosFCmat.R
fcros/R/chrMerge.R
fcros/R/fvalTopN.R
fcros/R/chrPlot2.R
fcros/R/chrSegment.R
fcros/R/fcrosTopN.R
fcros/R/rmatCalc.R
fcros/R/fc2Calc.R
fcros/R/pfcoMod.R
fcros/R/pvalTopN.R
fcros/R/fvalVolcanoPlot.R
fcros/R/rmatTrim.R
fcros/R/fcrosC.R
fcros/MD5
fcros/DESCRIPTION
fcros/man
fcros/man/fcros.Rd
fcros/man/fvalTopN.rd
fcros/man/chrMerge.rd
fcros/man/tprobaCalc.rd
fcros/man/cghInfo.Rd
fcros/man/dataSummary.rd
fcros/man/fcrosWrite.Rd
fcros/man/pvalTopN.rd
fcros/man/fcrosFCmat.Rd
fcros/man/fvalVolcanoPlot.rd
fcros/man/pvalVolcanoPlot.rd
fcros/man/fcrosTtest.Rd
fcros/man/chrPlot.rd
fcros/man/pfcoMod.rd
fcros/man/voomReads.rd
fcros/man/fcros-package.Rd
fcros/man/chrPlot2.rd
fcros/man/rmatTrim.rd
fcros/man/moyStdCalc.rd
fcros/man/fcrosRead.Rd
fcros/man/fcros2.Rd
fcros/man/histoPlot.rd
fcros/man/fc2Calc.rd
fcros/man/fcrosTopN.Rd
fcros/man/pfco.rd
fcros/man/cghData.Rd
fcros/man/fdata.Rd
fcros/man/fcrosC.Rd
fcros/man/chrSegment.rd
fcros/man/fcrosMod.Rd
fcros/man/rmatCalc.rd