beadarraySNP: Normalization and reporting of Illumina SNP bead arrays

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

AuthorJan Oosting
Date of publicationNone
MaintainerJan Oosting <j.oosting@lumc.nl>
LicenseGPL-2
Version1.40.0

View on Bioconductor

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

alterCN Man page
arrayID Man page
arrayID<- Man page
arrayID<-,QCIllumina-method Man page
arrayID,QCIllumina-method Man page
arrayType Man page
arrayType<- Man page
arrayType<-,QCIllumina-method Man page
arrayType,QCIllumina-method Man page
backgroundCorrect.SNP Man page
backgroundEstimate Man page
BeadstudioQC Man page
calculateGSR Man page
calculateGSR,SnpSetIllumina-method Man page
calculateLair Man page
calculateLOH Man page
calculateQCarray Man page
calculateSmooth Man page
calculateSmooth,SnpSetIllumina,character-method Man page
chr17.260 Man page
class:SnpSetIllumina Man page
cn.segments Man page
cn.segments<- Man page
cn.segments<-,SnpSetSegments,list-method Man page
cn.segments,SnpSetSegments-method Man page
combine,SnpSetIllumina,ANY-method Man page
combine,SnpSetIllumina,SnpSetIllumina-method Man page
compareGenotypes Man page
convert2aCGH Man page
convert2SegList Man page
createCNSummary Man page
dist.GT Man page
exprs<-,SnpSetIllumina,matrix-method Man page
exprs,SnpSetIllumina-method Man page
fData<-,SnpSetIllumina,data.frame-method Man page
fData,SnpSetIllumina-method Man page
featureData<-,SnpSetIllumina-method Man page
featureData,SnpSetIllumina-method Man page
GetBeadStudioSampleNames Man page
getDNAindex Man page
heterozygosity Man page
heterozygousSNPs Man page
initialize,QCIllumina-method Man page
initialize,SnpSetIllumina-method Man page
initialize,SnpSetSegments-method Man page
interactiveCNselect Man page
normalizeBetweenAlleles.SNP Man page
normalizeBetweenSubsamples.SNP Man page
normalizeLoci.SNP Man page
normalizeWithinArrays.SNP Man page
pdfBeadstudioQC Man page
pdfChromosomeGainLossLOH Man page
pdfChromosomesSmoothCopyNumber Man page
pdfQC Man page
pdfSamplesSmoothCopyNumber Man page
plotGenomePanels Man page
plotGoldenGate4OPA Man page
plotQC Man page
plotQC,QCIllumina-method Man page
polar2RG Man page
QC.260 Man page
QCIllumina Man page
QCIllumina-class Man page
read.SnpSetIllumina Man page
removeLowQualityProbes Man page
removeLowQualitySamples Man page
renameOPA Man page
reportChromosomeGainLossLOH Man page
reportChromosomesSmoothCopyNumber Man page
reportGenomeGainLossLOH Man page
reportGenomeIntensityPlot Man page
reportGenotypeSegmentation Man page
reportSamplePanelQC Man page
reportSamplePanelQC-methods Man page
reportSamplePanelQC,QCIllumina-method Man page
reportSamplesSmoothCopyNumber Man page
RG2polar Man page
Sample_Map2Samplesheet Man page
segmentate Man page
setRealCN Man page
smoothed.intensity Man page
SnpSetIllumina Man page
SnpSetIllumina-class Man page
[,SnpSetIllumina-method Man page
SnpSetSegments-class Man page
sortGenomic Man page
sortGenomic,SnpSetIllumina-method Man page
standardNormalization Man page

Files

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

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

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