Man pages for benilton/crlmm-release
Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays.

ABpanelA panel function for plotting prediction regions and...
AssayData-methodsMethods for class "AssayData" in crlmm
batchStatisticAccessorsAccessors for batch-specific summary statistics.
calculateRBafCalculate log R ratios and B allele frequencies.
celfile-utilsReads cel files and return an error if a file is not read
cnrmaAffyquantile normalize nonpolymorphic markers
cnSetExampleObject of class 'CNSet'
CNSet-methodscrlmm methods for class "CNSet"
constructAffyCNSetConstruct an object of class CNSet from Affymetrix cel files
constructInfInstantiate an object of class CNSet for the Infinium...
copynumberAccessorsAccessors for allele-specific or total copy number
crlmmGenotype oligonucleotide arrays with CRLMM
crlmmCopynumberLocus- and allele-specific estimation of copy number
crlmmIlluminaGenotype Illumina Infinium II BeadChip data with CRLMM
crlmmIlluminaV2Read and Genotype Illumina Infinium II BeadChip data with...
crlmm-packageGenotype Calling via CRLMM Algorithm
genotypePreprocessing and genotyping of Affymetrix arrays.
genotypeAffyGenotype Affymetrix CEL files
genotype.IlluminaPreprocessing and genotyping of Illumina Infinium II arrays.
genotypeInfGenotyping of Illumina Infinium II arrays.
genotypesThe possible genotypes for an integer copy number.
ListClassConstructorsMethods for Function 'BafLrrSetList' in Package 'crlmm' ~~
posteriorProbabilityCalculate the posterior probability for integer copy numbers.
predictionRegionPrediction regions for integer copy number
PredictionRegion-classClass '"PredictionRegion"'
preprocessInfPreprocessing of Illumina Infinium II arrays.
readGenCallOutputRead X and Y intensities from GenCall output
readIdatFilesReads Idat Files from Infinium II Illumina BeadChips
snprmaPreprocessing tool for SNP arrays.
snprmaAffyQuantile normalize intensities for SNPs
validCdfNamesSupported annotation packages for crlmm genotyping
xyplotPlot prediction regions and normalized intensities.
benilton/crlmm-release documentation built on May 11, 2017, 4:18 a.m.