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.

Author
Lasse Folkersen, Diego Diez
Date of publication
None
Maintainer
Lasse Folkersen <lasfol@cbs.dtu.dk>
License
GPL (>= 2)
Version
1.30.0

View on Bioconductor

Man pages

exampleProbeLevelSet
Example Dataset of class 'ProbeLevelSet'
excludeDoubleMatchingProbes
Exclude ProbeLevelSet probes that match more than once in...
findSequenceInGenome
Find a sequence in genome
genomic
genomic sequence of gene in ProbeLevelSet
mrna
mRNA sequence of gene in ProbeLevelSet
Nondocumented-objects
Here goes every undocumented function.
ProbeLevelSet-class
Class ProbeLevelSet

Files in this package

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