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crlmm (version 1.30.0)
Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays.
Description
Faster implementation of CRLMM specific to SNP 5.0 and 6.0 arrays, as well as a copy number tool specific to 5.0, 6.0, and Illumina platforms
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Version
Version
1.30.0
1.28.0
1.26.0
1.24.0
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Version
1.30.0
License
Artistic-2.0
Maintainer
Benilton Carvalho
Last Published
January 1st, 1970
Functions in crlmm (1.30.0)
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CNSet-methods
crlmm methods for class "CNSet"
cnSetExample
Object of class 'CNSet'
crlmmIlluminaV2
Read and Genotype Illumina Infinium II BeadChip data with CRLMM
crlmmIllumina
Genotype Illumina Infinium II BeadChip data with CRLMM
PredictionRegion-class
Class
"PredictionRegion"
posteriorProbability
Calculate the posterior probability for integer copy numbers.
ABpanel
A panel function for plotting prediction regions and log-normalized intensities
cnrmaAffy
quantile normalize nonpolymorphic markers
validCEL
Reads cel files and return an error if a file is not read
crlmm
Genotype oligonucleotide arrays with CRLMM
snprma
Preprocessing tool for SNP arrays.
crlmmCopynumber
Locus- and allele-specific estimation of copy number
snprmaAffy
Quantile normalize intensities for SNPs
AssayData-methods
Methods for class "AssayData" in crlmm
copynumberAccessors
Accessors for allele-specific or total copy number
crlmm-package
Genotype Calling via CRLMM Algorithm
genotypes
The possible genotypes for an integer copy number.
ListClassConstructors
Methods for Function
BafLrrSetList
in Package
crlmm
~~
validCdfNames
Supported annotation packages for crlmm genotyping
xyplot
Plot prediction regions and normalized intensities.
genotype.Illumina
Preprocessing and genotyping of Illumina Infinium II arrays.
genotype
Preprocessing and genotyping of Affymetrix arrays.
readGenCallOutput
Read X and Y intensities from GenCall output
readIdatFiles
Reads Idat Files from Infinium II Illumina BeadChips
batchStatisticAccessors
Accessors for batch-specific summary statistics.
calculateRBaf
Calculate log R ratios and B allele frequencies.
constructAffyCNSet
Construct an object of class CNSet from Affymetrix cel files
constructInf
Instantiate an object of class CNSet for the Infinium platforms.
genotypeAffy
Genotype Affymetrix CEL files
genotypeInf
Genotyping of Illumina Infinium II arrays.
predictionRegion
Prediction regions for integer copy number
preprocessInf
Preprocessing of Illumina Infinium II arrays.