beadarraySNP: Normalization and reporting of Illumina SNP bead arrays

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

Author
Jan Oosting
Date of publication
None
Maintainer
Jan Oosting <j.oosting@lumc.nl>
License
GPL-2
Version
1.40.0

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