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The possible genotypes for an integer copy number (0-4).
● Data Source:
BioConductor
● Keywords: manip
● Alias: genotypes
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posteriorProbability
(Package: crlmm) :
Calculate the posterior probability for integer copy numbers.
Calculate the posterior probability for integer copy numbers using the bivariate normal prediction regions.
● Data Source:
BioConductor
● Keywords: array
● Alias: posteriorProbability, posteriorProbability,CNSet-method
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0 images
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predictionRegion
(Package: crlmm) :
Prediction regions for integer copy number
Bivariate normal prediction regions for integer copy number. Copy numbers 0-4 allowed.
● Data Source:
BioConductor
● Keywords: distribution, list
● Alias: predictionRegion, predictionRegion,CNSet,integer-method
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0 images
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This function normalizes the intensities for the 'A' and 'B' alleles for a CNSet object and estimates mixture parameters used for subsequent genotyping. See details for how the normalized intensities are written to file. This step is required for subsequent genotyping and copy number estimation.
● Data Source:
BioConductor
● Keywords: manip
● Alias: preprocessInf
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0 images
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readGenCallOutput
(Package: crlmm) :
Read X and Y intensities from GenCall output
This function reads the raw X and Y intensities output by GenomeStudio's GenCall genotyping module in preparation for genotyping with crlmm.
● Data Source:
BioConductor
● Keywords: IO
● Alias: readGenCallOutput
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0 images
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readIdatFiles
(Package: crlmm) :
Reads Idat Files from Infinium II Illumina BeadChips
Reads intensity information for each bead type from .idat files of Infinium II genotyping BeadChips
● Data Source:
BioConductor
● Keywords: IO
● Alias: readIdatFiles, readIdatFiles2
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0 images
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SNPRMA will preprocess SNP chips. The preprocessing consists of quantile normalization to a known target distribution and summarization to the SNP-Allele level.
● Data Source:
BioConductor
● Keywords: classif, manip
● Alias: snprma, snprma2
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0 images
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snprmaAffy
(Package: crlmm) :
Quantile normalize intensities for SNPs
Quantile normalize intensities for SNPs to a HapMap target reference distribution
● Data Source:
BioConductor
● Keywords: robust
● Alias: snprmaAffy
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0 images
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validCdfNames
(Package: crlmm) :
Supported annotation packages for crlmm genotyping
Supported annotation packages for crlmm genotyping
● Data Source:
BioConductor
● Keywords: manip
● Alias: validCdfNames
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0 images
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xyplot
(Package: crlmm) :
Plot prediction regions and normalized intensities.
Plot prediction regions for integer copy number and normalized intensities.
● Data Source:
BioConductor
● Keywords: dplot, hplot
● Alias: xyplot, xyplot,formula,CNSet-method
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