Learn R Programming

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

Copy Link

Version

Version

1.30.0

License

Artistic-2.0

Maintainer

Benilton Carvalho

Last Published

February 15th, 2017

Functions in crlmm (1.30.0)

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.