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beadarraySNP (version 1.38.0)

Normalization and reporting of Illumina SNP bead arrays

Description

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

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Version

Version

1.38.0

License

GPL-2

Maintainer

Jan Oosting

Last Published

February 15th, 2017

Functions in beadarraySNP (1.38.0)

heterozygosity

Find regions of homozygous SNPs
copynumberConversion

Conversion to Copynumber analysis objects
backgroundEstimate

Estimate background intensities from foreground intensity
getDNAindex

Calculate the DNA index based on assigned copy number values to probes
Illumina Genomic data

Illumina example data
read.SnpSetIllumina

Read Experimental Data, Featuredata and Phenodata into an 'SnpSetIllumina' Object
alterCN

alterCN
dist.GT

dist.GT
segmentate

Segmentation for SnpSetIllumina objects
Sample_Map2Samplesheet

Convert Beadstudio Sample Map file to samplesheet
GetBeadStudioSampleNames

Extract samplenames from a report file
reportSamplePanelQC-methods

reportSamplePanelQC
plotQC

Spatial plots of array QC information
calculateQCarray

Retrieve QC information from a SnpSetIllumina object
reportGenotypeSegmentation

plot genomic view
setRealCN

Integrate state information into SNP object
BeadstudioQC

Quality control of Beadstudio report files
plotGoldenGate4OPA

Plot Golden Gate genomic view
QCIllumina-class

Class "QCIllumina"
GenomicReports

Genomic reports
backgroundCorrect.SNP

Background correction
normalizeBetweenAlleles.SNP

between Allele normalization
compareGenotypes

Compare genotypes
createCNSummary

Summarization of Copy number states
PolarTransforms

Polar transformations
QCaccessors

Accessor methods for QC objects
renameOPA

Change the linkage panel in a dataset
normalizeLoci.SNP

locus normalization
pdfChromosomesSmoothCopyNumber

reportWrappers
calculateLOH

Determine LOH in experiment
interactiveCNselect

Interactive assignment of copynumbers to genomic segments
SnpSetIllumina

Class to Contain Objects Describing High-Throughput SNP Assays.
normalizeBetweenSubsamples.SNP

Normalization between subsamples
standardNormalization

Default complete normalization
SnpSetSegments-class

Class "SnpSetSegments"
heterozygousSNPs

Retrieve heterozygous SNPs
removeLowQualitySamples

Quality control of SnpSetIllumina objects
normalizeWithinArrays.SNP

Within Array normalization
pdfQC

QCreport
smoothed.intensity

Smooth intensity data
removeLowQualityProbes

Quality control of SnpSetIllumina objects