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

Files in this package

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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