GeneRegionScan: GeneRegionScan

A package with focus on analysis of discrete regions of the genome. This package is useful for investigation of one or a few genes using Affymetrix data, since it will extract probe level data using the Affymetrix Power Tools application and wrap these data into a ProbeLevelSet. A ProbeLevelSet directly extends the expressionSet, but includes additional information about the sequence of each probe and the probe set it is derived from. The package includes a number of functions used for plotting these probe level data as a function of location along sequences of mRNA-strands. This can be used for analysis of variable splicing, and is especially well suited for use with exon-array data.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("GeneRegionScan")
AuthorLasse Folkersen, Diego Diez
Bioconductor views DataImport Microarray OneChannel SNP Visualization
Date of publicationNone
MaintainerLasse Folkersen <lasfol@cbs.dtu.dk>
LicenseGPL (>= 2)
Version1.30.0

View on Bioconductor

Files

BinaryFiles
DESCRIPTION
NAMESPACE
R
R/ProbeLevelSet-class.R R/ProbeLevelSet-methods.R R/analysisFunctions.R R/creationFunctions.R
TODO
build
build/vignette.rds
data
data/exampleProbeLevelSet.rdata
exec
exec/apt-cel-extract-linux64
exec/apt-cel-extract-win32.exe
exec/apt-probeset-summarize-win32.exe
inst
inst/CITATION
inst/configfiles
inst/configfiles/aptextractfiles.txt
inst/configfiles/aptsummarizefiles.txt
inst/configfiles/locations.txt
inst/doc
inst/doc/GeneRegionScan.R
inst/doc/GeneRegionScan.Rnw
inst/doc/GeneRegionScan.pdf
inst/translationfiles
inst/translationfiles/GSE9372_name_translation.txt
man
man/Nondocumented-objects.Rd man/ProbeLevelSet-class.Rd
man/addSnpPdata.rd
man/checkForFileInPath.rd
man/doProbeLinear.rd
man/doProbeTTest.rd
man/exampleProbeLevelSet.Rd man/excludeDoubleMatchingProbes.Rd
man/exonStructure.rd
man/findProbePositions.rd
man/findSequenceInGenome.Rd
man/geneRegionScan.rd
man/genomic.Rd
man/getLocalMetaprobeIntensities.rd
man/getLocalProbeIntensities.rd
man/getMetaprobesetsFromRegionOfInterest.rd
man/getProbeLevelAnnotationForExonArrays.rd
man/getProbesetsFromMetaprobeset.rd
man/getProbesetsFromRegionOfInterest.rd
man/getSequence.rd
man/getServerProbeIntensities.rd
man/mrna.Rd
man/plotCoexpression.rd
man/plotOnGene.rd
man/plotStatistics.rd
man/readGeneInput.rd
man/translateSampleNames.rd
vignettes
vignettes/GeneRegionScan.Rnw

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

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