GeneRegionScan: GeneRegionScan
Version 1.32.0

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.

Browse man pages Browse package API and functions Browse package files

AuthorLasse Folkersen, Diego Diez
Bioconductor views DataImport Microarray OneChannel SNP Visualization
Date of publicationNone
MaintainerLasse Folkersen <lasfol@cbs.dtu.dk>
LicenseGPL (>= 2)
Version1.32.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("GeneRegionScan")

Man pages

addSnpPdata: Add SNP data from hapmap-style data file to pData of...
checkForFileInPath: Check For File In Path
doProbeLinear: Do Probe Linear
doProbeTTest: Do Probe T-Test
exampleProbeLevelSet: Example Dataset of class 'ProbeLevelSet'
excludeDoubleMatchingProbes: Exclude ProbeLevelSet probes that match more than once in...
exonStructure: Add exon-structure to plots
findProbePositions: Find positions of probes on a gene
findSequenceInGenome: Find a sequence in genome
geneRegionScan: Gene Region Scan
genomic: genomic sequence of gene in ProbeLevelSet
getLocalMetaprobeIntensities: Get Metaprobe Intensities locally
getLocalProbeIntensities: Get Probe Intensities locally
getMetaprobesetsFromRegionOfInterest: Get Meta Probe Set IDs From Region Of Interest
getProbeLevelAnnotationForExonArrays: Get ProbeLevel Annotation for Exon Arrays
getProbesetsFromMetaprobeset: Get Probeset IDs From metaprobeset IDs
getProbesetsFromRegionOfInterest: Get Probeset IDs From Region Of Interest
getSequence: Get Sequence from a ProbeLevelSet
getServerProbeIntensities: Get Probe Intensities from a server
mrna: mRNA sequence of gene in ProbeLevelSet
Nondocumented-objects: Here goes every undocumented function.
plotCoexpression: Plot Coexpression of probes in a ProbeLevelSet
plotOnGene: Plot probe level data on a gene
plotStatistics: Plot Statistics
ProbeLevelSet-class: Class ProbeLevelSet
readGeneInput: Standardize reading of gene inputs
translateSampleNames: Translate sample names using translation file

Functions

GeneRegionScan Man page
Nondocumented-objects Man page
ProbeLevelSet Man page
ProbeLevelSet-class Man page
addSnpPdata Man page
addSnpPdata,ExpressionSet-method Man page
checkForFileInPath Man page Source code
createFeatureData Source code
doProbeLinear Man page
doProbeTTest Man page
exampleProbeLevelSet Man page
excludeDoubleMatchingProbes Man page
excludeDoubleMatchingProbes,ProbeLevelSet-method Man page
exonStructure Man page Source code
findProbePositions Man page
findProbePositions,ExpressionSet-method Man page
findSequenceInGenome Man page Source code
geneRegionScan Man page
geneRegionScan,ExpressionSet-method Man page
genomic Man page
getLocalMetaprobeIntensities Man page Source code
getLocalProbeIntensities Man page Source code
getMetaprobesetsFromRegionOfInterest Man page Source code
getProbeLevelAnnotationForExonArrays Man page Source code
getProbesetsFromMetaprobeset Man page Source code
getProbesetsFromRegionOfInterest Man page Source code
getSequence Man page
getSequence,ProbeLevelSet-method Man page
getServerProbeIntensities Man page Source code
mrna Man page
plotCoexpression Man page
plotCoexpression,ExpressionSet-method Man page
plotOnGene Man page
plotOnGene,ExpressionSet-method Man page
plotStatistics Man page
readFASTA_replacement Source code
readGeneInput Man page Source code
translateSampleNames Man page
translateSampleNames,ExpressionSet-method Man page

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
GeneRegionScan documentation built on May 20, 2017, 10:55 p.m.