Man pages for crlmm
Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays
| ABpanel | A panel function for plotting prediction regions and... |
| AssayData-methods | Methods for class "AssayData" in crlmm |
| batchStatisticAccessors | Accessors for batch-specific summary statistics. |
| calculateRBaf | Calculate log R ratios and B allele frequencies. |
| celfile-utils | Reads cel files and return an error if a file is not read |
| cnrmaAffy | quantile normalize nonpolymorphic markers |
| cnSetExample | Object of class 'CNSet' |
| CNSet-methods | 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... |
| copynumberAccessors | Accessors for allele-specific or total copy number |
| crlmm | Genotype oligonucleotide arrays with CRLMM |
| crlmmCopynumber | Locus- and allele-specific estimation of copy number |
| crlmm-package | Genotype Calling via CRLMM Algorithm |
| genotype | Preprocessing and genotyping of Affymetrix arrays. |
| genotypeAffy | Genotype Affymetrix CEL files |
| genotype.Illumina | Preprocessing and genotyping of Illumina Infinium II arrays. |
| genotypeInf | Genotyping of Illumina Infinium II arrays. |
| genotypes | The possible genotypes for an integer copy number. |
| ListClassConstructors | Methods for Function 'BafLrrSetList' in Package 'crlmm' ~~ |
| plotSNPs | Make M vs S plot for SNPs or samples. |
| posteriorProbability | Calculate the posterior probability for integer copy numbers. |
| predictionRegion | Prediction regions for integer copy number |
| PredictionRegion-class | Class '"PredictionRegion"' |
| preprocessInf | Preprocessing of Illumina Infinium II arrays. |
| readGenCallOutput | Read X and Y intensities from GenCall output |
| readIdatFiles | Reads Idat Files from Infinium II Illumina BeadChips |
| snprma | Preprocessing tool for SNP arrays. |
| snprmaAffy | Quantile normalize intensities for SNPs |
| validCdfNames | Supported annotation packages for crlmm genotyping |
| xyplot | Plot prediction regions and normalized intensities. |
