gada: Genome Alteration Detection Algorithm (GADA)

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.

AuthorJuan R Gonzalez, Roger Pique-Regi and Alejandro Caceres
Date of publicationNone
MaintainerJuan R Gonzalez <jrgonzalez@creal.cat>
LicenseGPL version 2 or newer
Version1.0
http://groups.google.com/group/gadaproject and http://www.creal.cat/jrgonzalez/software

View on R-Forge

Functions

addGadaToAromaAffymetrix Man page
assocCNV.i Man page
BackwardElimination Man page
BackwardElimination.fit Man page
collapseInfo Man page
countAltered.i Man page
discriminCNV Man page
drawChromosome Man page
drawChromosomeZoom Man page
dudi.acm.fortran Man page
exportToBED Man page
findNormalLimits Man page
gada Man page
gada-internal Man page
gada-package Man page
getAlteredProbes Man page
getChromosomeDat Man page
get.index Man page
get.matrix Man page
getNamesProbes Man page
getProj Man page
getPvalBH Man page
getReducedData Man page
ideogram Man page
labels.parGADA Man page
labels.summaryParGADA Man page
matrixPlot Man page
multiCNVassoc Man page
parBE Man page
parSBL Man page
plapply Man page
plot.cnv.discrimin Man page
plotlogRatio Man page
plot.multiCNVassoc Man page
plotRatio Man page
plotRatio.BackwardElimination Man page
plotRatio.parGADA Man page
plotRatio.setupGADA Man page
plotWG Man page
print.BackwardElimination Man page
print.cnv.discrimin Man page
print.SBL Man page
print.summaryParGADA Man page
project.pop Man page
rankVariables Man page
reduceMatrix Man page
SBL Man page
SBL.fit Man page
selectSegment Man page
setupGADAaffy Man page
setupGADAgeneral Man page
setupGADAIllumina Man page
setupParGADAaffy Man page
setupParGADAIllumina Man page
sortPopData Man page
splitDataBeadStudio Man page
summary.BackwardElimination Man page
summary.parGADA Man page
tamanysChroms Man page
WextIextToSegments Man page

Files

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.