# Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays

## Documentation for package ‘crlmm’ version 1.38.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

crlmm-package | Genotype Calling via CRLMM Algorithm
ABpanel | A panel function for plotting prediction regions and log-normalized intensities
BafLrrSetList | Methods for Function 'BafLrrSetList' in Package 'crlmm' ~~
BafLrrSetList-method | crlmm methods for class "CNSet"
CA | Accessors for allele-specific or total copy number
CA-method | crlmm methods for class "CNSet"
calculateRBaf | Calculate log R ratios and B allele frequencies.
calculateRBaf-method | Calculate log R ratios and B allele frequencies.
CB | Accessors for allele-specific or total copy number
CB-method | crlmm methods for class "CNSet"
celDates | Reads cel files and return an error if a file is not read
cnrmaAffy | quantile normalize nonpolymorphic markers
cnSetExample | Object of class 'CNSet'
cnSetExample2 | Object of class 'CNSet'
coerce-method | crlmm methods for class "CNSet"
constructAffyCNSet | Construct an object of class CNSet from Affymetrix cel files
constructInf | Instantiate an object of class CNSet for the Infinium platforms.
corr | Accessors for batch-specific summary statistics.
corr-method | Methods for class "AssayData" in crlmm
corr-method | crlmm methods for class "CNSet"
crlmm | Genotype oligonucleotide arrays with CRLMM
crlmm2 | Genotype oligonucleotide arrays with CRLMM
crlmmCopynumber | Locus- and allele-specific estimation of copy number
crlmmCopynumber2 | Locus- and allele-specific estimation of copy number
crlmmCopynumberLD | Locus- and allele-specific estimation of copy number
crlmmIllumina | Preprocessing and genotyping of Illumina Infinium II arrays.
genotype | Preprocessing and genotyping of Affymetrix arrays.
genotype.Illumina | Preprocessing and genotyping of Illumina Infinium II arrays.
genotype2 | Preprocessing and genotyping of Affymetrix arrays.
genotypeAffy | Genotype Affymetrix CEL files
genotypeInf | Genotyping of Illumina Infinium II arrays.
genotypeLD | Preprocessing and genotyping of Affymetrix arrays.
genotypes | The possible genotypes for an integer copy number.
lines-method | crlmm methods for class "CNSet"
mads | Accessors for batch-specific summary statistics.
mads-method | Methods for class "AssayData" in crlmm
mads-method | crlmm methods for class "CNSet"
medians | Accessors for batch-specific summary statistics.
medians-method | Methods for class "AssayData" in crlmm
medians-method | crlmm methods for class "CNSet"
Ns | Accessors for batch-specific summary statistics.
Ns-method | Methods for class "AssayData" in crlmm
Ns-method | crlmm methods for class "CNSet"
nuA | Accessors for allele-specific or total copy number
nuA-method | crlmm methods for class "CNSet"
nuB | Accessors for allele-specific or total copy number
nuB-method | crlmm methods for class "CNSet"
OligoSetList | Methods for Function 'BafLrrSetList' in Package 'crlmm' ~~
OligoSetList-method | crlmm methods for class "CNSet"
phiA | Accessors for allele-specific or total copy number
phiA-method | crlmm methods for class "CNSet"
phiB | Accessors for allele-specific or total copy number
phiB-method | crlmm methods for class "CNSet"
plotSamples | Make M vs S plot for SNPs or samples.
plotSNPs | Make M vs S plot for SNPs or samples.
posteriorProbability | Calculate the posterior probability for integer copy numbers.
posteriorProbability-method | Calculate the posterior probability for integer copy numbers.
predictionRegion | Prediction regions for integer copy number
PredictionRegion-class | Class '"PredictionRegion"'
predictionRegion-method | Prediction regions for integer copy number
preprocessInf | Preprocessing of Illumina Infinium II arrays.
rawCopynumber | Accessors for allele-specific or total copy number
rawCopynumber-method | crlmm methods for class "CNSet"
readGenCallOutput | Read X and Y intensities from GenCall output
readIdatFiles | Reads Idat Files from Infinium II Illumina BeadChips
readIdatFiles2 | Reads Idat Files from Infinium II Illumina BeadChips
snprma | Preprocessing tool for SNP arrays.
snprma2 | Preprocessing tool for SNP arrays.
snprmaAffy | Quantile normalize intensities for SNPs
tau2 | Accessors for batch-specific summary statistics.
tau2-method | Methods for class "AssayData" in crlmm
tau2-method | crlmm methods for class "CNSet"
totalCopynumber | Accessors for allele-specific or total copy number
totalCopynumber-method | crlmm methods for class "CNSet"
validCdfNames | Supported annotation packages for crlmm genotyping
validCEL | Reads cel files and return an error if a file is not read
xyplot | Plot prediction regions and normalized intensities.
xyplot-method | Plot prediction regions and normalized intensities.
[-method | Class '"PredictionRegion"'