Package: fcros 1.6-6

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

A fold change rank based method is presented to search for genes with changing expression and to detect recurrent chromosomal copy number aberrations. This method may be useful for high-throughput biological data (micro-array, sequencing, ...). Probabilities are associated with genes or probes in the data set and there is no problem of multiple tests when using this method. For array-based comparative genomic hybridization data, segmentation results are obtained by merging the significant probes detected.

Authors:Doulaye Dembele [aut, cre]

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manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
fcros/json (API)

# Install 'fcros' in R:
install.packages('fcros', repos = c('https://doulaye.r-universe.dev', 'https://cloud.r-project.org'))
Datasets:
  • bott - Example of sequencing data to test the rankReads function.
  • cghData - Example of aCGH "data file" for the fcros package.
  • cghInfo - Example of aCGH "info file" for the fcros package.
  • fdata - Example of dataset for the fcros package.

On CRAN:

Conda:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

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Last updated from:d7f11381e8. Checks:15 OK. Indexed: yes.

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Exports:calcSRmatcalcSRmatModchrMergechrPlotchrPlot2chrSegmentdataSummaryfc2Calcfcrosfcros2fcrosFCmatfcrosModfcrosReadfcrosTopNfcrosTtestfcrosWritefvalTopNfvalVolcanoPlothistoPlotmoyStdCalcpfcopfcoModpvalTopNpvalVolcanoPlotrankReadsrmatCalcrmatTrimscoreThrtcnReadstprobaCalcvarBetavoomReads

Dependencies:

Readme and manuals

Help Manual

Help pageTopics
A Method to Search for Differentially Expressed Genes and to Detect Recurrent Chromosomal Copy Number Aberrationsfcros-package
Example of sequencing data to test the rankReads function.bott
Calculation of the sorted rank matrix from the datasetcalcSRmat
Calculation of the sorted rank matrix from the datasetcalcSRmatMod
Example of aCGH "data file" for the fcros package.cghData
Example of aCGH "info file" for the fcros package.cghInfo
Using a C code for merging chromosome segmentschrMerge
Plot a chromosome datachrPlot
Plot a chromosome segmentation resultschrPlot2
Segmentation of a chromosome datachrSegment
Summarization of the detection results for a list of chromosomesdataSummary
Calculation of fold change using pairwise comparison valuesfc2Calc
Search for differentially expressed genes/probesfcros
Search for differentially expressed genes/probesfcros2
Search for differentially expressed genes/probesfcrosC
Calculation of a matrix of fold changes using pairwise comparisonsfcrosFCmat
Search for differentially expressed genes or to detect recurrent copy number aberration probesfcrosMod
Read a tab delimited text filefcrosRead
Search for the top N changed genes or probesfcrosTopN
Student t-test for detecting differentially expressed genesfcrosTtest
Writing the fcros() or pfco() results in a tab delimited text filefcrosWrite
Example of dataset for the fcros package.fdata
Search for the top N changed genes or probes using f-valuesfvalTopN
Performs a volcano plot of the FCROS/PFCO statisticsfvalVolcanoPlot
Histogram plot function of the fcros package resultshistoPlot
Calculation of the mean and the standard deviation of the full or reduced matrix of sorted ranksmoyStdCalc
Searching for differentially expressed genes/probes using an approach based on the Perron-Frobenius theorempfco
Searching for differentially expressed genes or detecting recurrent copy number aberration probes using an approach based on the Perron-Frobenius theorempfcoMod
Search for the top N changed genes or probes using p-valuespvalTopN
Performs a volcano plot of the FCROS/PFCO statisticspvalVolcanoPlot
This function computes a score to assess the significance of sequencing valuesrankReads
Calculation of the FC matrix using pairwise comparisonsrmatCalc
Calculation of the reduced matrix containing sorted rank valuesrmatTrim
Determine numerically a threshold for the ranking scorescoreThr
Performs a total count normalization of readstcnReads
Calculation of the Student one sample test probabilitiestprobaCalc
Compute variance of a beta distribution from datavarBeta
Transformation of read count valuesvoomReads