beadarraySNP: Normalization and reporting of Illumina SNP bead arrays
Version 1.42.0

Importing data from Illumina SNP experiments and performing copy number calculations and reports.

AuthorJan Oosting
Bioconductor views CopyNumberVariation DataImport GeneticVariability Preprocessing SNP TwoChannel
Date of publicationNone
MaintainerJan Oosting <j.oosting@lumc.nl>
LicenseGPL-2
Version1.42.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("beadarraySNP")

Popular man pages

backgroundCorrect.SNP: Background correction
calculateLOH: Determine LOH in experiment
calculateQCarray: Retrieve QC information from a SnpSetIllumina object
heterozygousSNPs: Retrieve heterozygous SNPs
normalizeLoci.SNP: locus normalization
pdfChromosomesSmoothCopyNumber: reportWrappers
plotQC: Spatial plots of array QC information
See all...

All man pages Function index File listing

Man pages

alterCN: alterCN
arrayType: Accessor methods for QC objects
backgroundCorrect.SNP: Background correction
backgroundEstimate: Estimate background intensities from foreground intensity
BeadstudioQC: Quality control of Beadstudio report files
calculateLOH: Determine LOH in experiment
calculateQCarray: Retrieve QC information from a SnpSetIllumina object
class.SnpSetIllumina: Class to Contain Objects Describing High-Throughput SNP...
compareGenotypes: Compare genotypes
CopynumberConversion: Conversion to Copynumber analysis objects
createCNSummary: Summarization of Copy number states
Datasets: Illumina example data
dist.GT: dist.GT
GenomicReports: Genomic reports
GetBeadStudioSampleNames: Extract samplenames from a report file
getDNAindex: Calculate the DNA index based on assigned copy number values...
heterozygosity: Find regions of homozygous SNPs
heterozygousSNPs: Retrieve heterozygous SNPs
interactiveCNselect: Interactive assignment of copynumbers to genomic segments
normalizeBetweenAlleles.SNP: between Allele normalization
normalizeBetweenSubsamples.SNP: Normalization between subsamples
normalizeLoci.SNP: locus normalization
normalizeWithinArrays.SNP: Within Array normalization
pdfChromosomesSmoothCopyNumber: reportWrappers
pdfQC: QCreport
plotGoldenGate4OPA: Plot Golden Gate genomic view
plotQC: Spatial plots of array QC information
PolarTransforms: Polar transformations
QCIllumina-class: Class "QCIllumina"
read.SnpSetIllumina: Read Experimental Data, Featuredata and Phenodata into an...
removeLowQualityProbes: Quality control of SnpSetIllumina objects
removeLowQualitySamples: Quality control of SnpSetIllumina objects
renameOPA: Change the linkage panel in a dataset
reportGenotypeSegmentation: plot genomic view
reportSamplePanelQC-methods: reportSamplePanelQC
Sample_Map2Samplesheet: Convert Beadstudio Sample Map file to samplesheet
segmentate: Segmentation for SnpSetIllumina objects
setRealCN: Integrate state information into SNP object
smoothed.intensity: Smooth intensity data
SnpSetSegments-class: Class "SnpSetSegments"
standardNormalization: Default complete normalization

Functions

BeadstudioQC Man page Source code
GetBeadStudioSampleNames Man page Source code
IlluminaGetGencalls Source code
IlluminaGetOPAinfo Source code
QC.260 Man page
QCIllumina Man page
QCIllumina-class Man page
RG2polar Man page Source code
Sample_Map2Samplesheet Man page Source code
SnpSetIllumina Man page
SnpSetIllumina-class Man page
SnpSetSegments-class Man page
[,SnpSetIllumina-method Man page
alterCN Man page Source code
arrayID Man page
arrayID,QCIllumina-method Man page
arrayID<- Man page
arrayID<-,QCIllumina-method Man page
arrayType Man page
arrayType,QCIllumina-method Man page
arrayType<- Man page
arrayType<-,QCIllumina-method Man page
backgroundCorrect.SNP Man page Source code
backgroundEstimate Man page Source code
calculateGSR Man page
calculateGSR,SnpSetIllumina-method Man page
calculateLOH Man page Source code
calculateLair Man page Source code
calculateQCarray Man page Source code
calculateSmooth Man page
calculateSmooth,SnpSetIllumina,character-method Man page
chr17.260 Man page
class:SnpSetIllumina Man page
cn.segments Man page
cn.segments,SnpSetSegments-method Man page
cn.segments<- Man page
cn.segments<-,SnpSetSegments,list-method Man page
combine,SnpSetIllumina,ANY-method Man page
combine,SnpSetIllumina,SnpSetIllumina-method Man page
compareGenotypes Man page Source code
convert2SegList Man page Source code
convert2aCGH Man page Source code
createCNSummary Man page Source code
dist.GT Man page Source code
exprs,SnpSetIllumina-method Man page
exprs<-,SnpSetIllumina,matrix-method Man page
fData,SnpSetIllumina-method Man page
fData<-,SnpSetIllumina,data.frame-method Man page
featureData,SnpSetIllumina-method Man page
featureData<-,SnpSetIllumina-method Man page
getAssayData Source code
getDNAindex Man page Source code
getExperiments Source code
getGrouping Source code
getMidMaxIdx Source code
getNorTum Source code
getSubsample Source code
heterozygosity Man page Source code
heterozygousSNPs Man page Source code
initialize,QCIllumina-method Man page
initialize,SnpSetIllumina-method Man page
initialize,SnpSetSegments-method Man page
interactiveCNselect Man page Source code
mergeAnnotateddata Source code
mergeAssayData Source code
mergefeatureData Source code
normalizeBetweenAlleles.SNP Man page Source code
normalizeBetweenSubsamples.SNP Man page Source code
normalizeLoci.SNP Man page Source code
normalizeWithinArrays.SNP Man page Source code
pdfBeadstudioQC Man page Source code
pdfChromosomeGainLossLOH Man page Source code
pdfChromosomesSmoothCopyNumber Man page Source code
pdfQC Man page Source code
pdfSamplesSmoothCopyNumber Man page Source code
plotGenomePanels Man page Source code
plotGoldenGate4OPA Man page Source code
plotGroupZygosity Source code
plotQC Man page
plotQC,QCIllumina-method Man page
polar2RG Man page Source code
read.SnpSetBeadstudio Source code
read.SnpSetGencall Source code
read.SnpSetIllumina Man page Source code
read.SnpSetSampleSheet Source code
readClusteringData Source code
readReportfile Source code
removeLowQualityProbes Man page Source code
removeLowQualitySamples Man page Source code
renameOPA Man page Source code
reportChromosomeGainLossLOH Man page Source code
reportChromosomesSmoothCopyNumber Man page Source code
reportGenomeGainLossLOH Man page Source code
reportGenomeIntensityPlot Man page Source code
reportGenotypeSegmentation Man page Source code
reportGroupZygosity Source code
reportSamplePanelQC Man page
reportSamplePanelQC,QCIllumina-method Man page
reportSamplePanelQC-methods Man page
reportSamplesSmoothCopyNumber Man page Source code
segmentate Man page Source code
segmentate.old Source code
setRealCN Man page Source code
smoothed.intensity Man page Source code
smoothed.probes Source code
smoothed.size Source code
sortGenomic Man page
sortGenomic,SnpSetIllumina-method Man page
standardNormalization Man page Source code

Files

DESCRIPTION
NAMESPACE
R
R/AllClasses.R
R/AllGenerics.R
R/SnpSetIlluminaConversion.r
R/SnpSetIlluminaGenotypes.R
R/SnpSetIlluminaInteractive.R
R/SnpSetIlluminaNormalize.R
R/SnpSetIlluminaQC.R
R/SnpSetIlluminaReports.R
R/SnpSetIlluminaSegment.R
R/SnpSetIlluminaSmoothing.r
R/methods-QCIllumina.R
R/methods-SnpSetIllumina.R
R/methods-SnpSetSegments.R
build
build/vignette.rds
data
data/QC.260.rda
data/chr17.260.rda
inst
inst/doc
inst/doc/beadarraySNP.R
inst/doc/beadarraySNP.pdf
inst/doc/beadarraySNP.rnw
inst/testdata
inst/testdata/11186795_GS0005704-OPA_LinkageIV_v3.opa
inst/testdata/1280260_R002_C012.csv
inst/testdata/1280260_R003_C012.csv
inst/testdata/1280260_R007_C010.csv
inst/testdata/1280260_R008_C010.csv
inst/testdata/4samples_opa4.csv
inst/testdata/GS0005704-OPA_LocusByDNA.csv
inst/testdata/targets.txt
man
man/BeadstudioQC.Rd
man/CopynumberConversion.Rd
man/Datasets.Rd
man/GenomicReports.Rd
man/GetBeadStudioSampleNames.Rd
man/PolarTransforms.Rd
man/QCIllumina-class.Rd
man/Sample_Map2Samplesheet.Rd
man/SnpSetSegments-class.Rd
man/alterCN.Rd
man/arrayType.Rd
man/backgroundCorrect.SNP.Rd
man/backgroundEstimate.Rd
man/calculateLOH.Rd
man/calculateQCarray.Rd
man/class.SnpSetIllumina.Rd
man/compareGenotypes.Rd
man/createCNSummary.Rd
man/dist.GT.Rd
man/getDNAindex.Rd
man/heterozygosity.Rd
man/heterozygousSNPs.Rd
man/interactiveCNselect.Rd
man/normalizeBetweenAlleles.SNP.Rd
man/normalizeBetweenSubsamples.SNP.Rd
man/normalizeLoci.SNP.Rd
man/normalizeWithinArrays.SNP.Rd
man/pdfChromosomesSmoothCopyNumber.Rd
man/pdfQC.Rd
man/plotGoldenGate4OPA.Rd
man/plotQC.Rd
man/read.SnpSetIllumina.Rd
man/removeLowQualityProbes.Rd
man/removeLowQualitySamples.Rd
man/renameOPA.Rd
man/reportGenotypeSegmentation.Rd
man/reportSamplePanelQC-methods.Rd
man/segmentate.Rd
man/setRealCN.Rd
man/smoothed.intensity.Rd
man/standardNormalization.Rd
vignettes
vignettes/beadarraySNP.rnw
beadarraySNP documentation built on May 20, 2017, 10:15 p.m.

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

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

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