gada: Genome Alteration Detection Algorithm (GADA)

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The package implements a flexible and efficient analysis pipeline to detect genomic copy number alterations from microarray data. It can import the raw copy number normalized intensities provided by Illumina BeadStudio, Affymetrix powertools, or any similar format. Probes of different samples are split into separate files and can be analyzed on a standalone workstation or in parallel using a cluster/multicore computer. The speed and accuracy of the genome alteration detection analysis (GADA) approach combined with parallel computing results in one of the fastest and most accurate methods, and it is especially suitable to extract copy number alterations (CNAs) on genomewide studies involving hundreds of samples utilizing high density arrays with millions of markers. Functions to perform multivariate analysis and determining common regions among individuals are implemented. Functions to assess association between CNVs blocks and disease is also provided. Useful tools for the summarization and visualization of the discovered CNA are also included.

Author
Juan R Gonzalez, Roger Pique-Regi and Alejandro Caceres
Date of publication
None
Maintainer
Juan R Gonzalez <jrgonzalez@creal.cat>
License
GPL version 2 or newer
Version
1.0
URLs

View on R-Forge

Man pages

addGadaToAromaAffymetrix
Connect gada and aroma.affymetrix packages
BackwardElimination
Backward Elimination of segmentation breakpoints
discriminCNV
Discrimination Analysis for CNV data matrices
dudi.acm.fortran
Duality diagram for Multiple Correspondenc Analysis
exportToBED
Export segments to BED format
gada-internal
Internal gada functions
gada-package
Genome Alteration Detection Algorithm (GADA)
getAlteredProbes
Get Altered Probes
getChromosomeDat
Cromosome CNV Data
getNamesProbes
CNVs with highes correlations
getPvalBH
Corrected p values using Benjamini & Hochberg approach
getReducedData
Reduced matrix of CNV blocks across the whole genome
matrixPlot
Matrix image of CNV blocks
multiCNVassoc
Association between several CNVs and disease
parBE
Parallel Backward Elimination
parSBL
Parallel SBL segmentation
plotRatio
Plot log2Ratio intensities
plotWG
Plot Whole Genome
rankVariables
CNV ranking
reduceMatrix
Reduction of matrix of CNV segments
SBL
Sparse Bayesian Learning (SBL) Segmentation Algorithm
setupGADAaffy
Imports Affymetrix array data to gada
setupGADAgeneral
Imports general array data to gada
setupGADAIllumina
Imports Illumina array data to gada
setupParGADAaffy
Parallel version of setupGADAaffy
setupParGADAIllumina
Parallel version of setupGADAIllumina
splitDataBeadStudio
Split BeadStudio data

Files in this package

gada
gada/data
gada/data/genomicInfo.rda
gada/R
gada/R/findNormalLimits.R
gada/R/drawChromosome.R
gada/R/getPvalBH.R
gada/R/getAlteredProbes.R
gada/R/get.index.R
gada/R/setupGADAIllumina.R
gada/R/selectSegment.R
gada/R/SBL.R
gada/R/plotlogRatio.R
gada/R/print.BackwardElimination.R
gada/R/dudi.acm.fortran.R
gada/R/discriminCNV.R
gada/R/project.pop.R
gada/R/WextIextToSegments.R
gada/R/rankVariables.R
gada/R/matrixPlot.R
gada/R/plot.acm.R
gada/R/plot.cnv.discrimin.R
gada/R/BackwardElimination.fit.R
gada/R/labels.parGADA.R
gada/R/plotRatio.R
gada/R/print.summaryParGADA.R
gada/R/getNamesProbes.R
gada/R/print.cnv.discrimin.R
gada/R/setupParGADAaffy.R
gada/R/print.SBL.R
gada/R/drawChromosomeZoom.R
gada/R/get.chromosome.dat.R
gada/R/assocCNV.i.R
gada/R/plot.summaryParGADA.R
gada/R/parSBL.R
gada/R/summary.BackwardElimination.R
gada/R/getProj.R
gada/R/firstlib.R
gada/R/BackwardElimination.R
gada/R/exportToBED.R
gada/R/setupParGADAIllumina.R
gada/R/plotRatio.parGADA.R
gada/R/plapply.R
gada/R/parBE.R
gada/R/summary.parGADA.R
gada/R/summary.list.R
gada/R/sortPopData.R
gada/R/multiCNVassoc.R
gada/R/collapseInfo.R
gada/R/splitDataBeadStudio.R
gada/R/get.matrix.R
gada/R/countAltered.i.R
gada/R/plotRatio.BackwardElimination.R
gada/R/GadaInAromaAffymetrix.R
gada/R/plotRatio.setupGADA.R
gada/R/plot.multiCNVassoc.R
gada/R/setupGADAgeneral.R
gada/R/setupGADAaffy.R
gada/R/reduceMatrix.R
gada/R/getChromosomeDat.R
gada/R/SBL.fit.R
gada/R/getReducedData.R
gada/R/print.setupGADA.R
gada/R/plotWG.R
gada/exec
gada/exec/addGadaToAromaAffymetrix.R
gada/exec/splitData.pl
gada/NAMESPACE
gada/inst
gada/inst/docs
gada/inst/docs/changelog.txt
gada/DESCRIPTION
gada/man
gada/man/addGadaToAromaAffymetrix.Rd
gada/man/setupParGADAaffy.Rd
gada/man/plotWG.Rd
gada/man/getAlteredProbes.Rd
gada/man/reduceMatrix.Rd
gada/man/setupGADAgeneral.Rd
gada/man/splitDataBeadStudio.Rd
gada/man/multiCNVassoc.Rd
gada/man/SBL.Rd
gada/man/getChromosomeDat.Rd
gada/man/setupGADAaffy.Rd
gada/man/setupParGADAIllumina.Rd
gada/man/getPvalBH.Rd
gada/man/gada-package.Rd
gada/man/rankVariables.Rd
gada/man/gada-internal.Rd
gada/man/matrixPlot.Rd
gada/man/parSBL.Rd
gada/man/parBE.Rd
gada/man/dudi.acm.fortran.Rd
gada/man/discriminCNV.Rd
gada/man/plotRatio.Rd
gada/man/exportToBED.Rd
gada/man/BackwardElimination.Rd
gada/man/getNamesProbes.Rd
gada/man/setupGADAIllumina.Rd
gada/man/getReducedData.Rd
gada/src
gada/src/floc.f
gada/src/gada.c
gada/src/Makevars
gada/src/BaseGADA.h
gada/src/RGADAdefines.h
gada/src/BaseGADA.c
gada/files
gada/files/kcolumn.pl