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

## Documentation for package ‘crlmm’ version 1.4.5

## User Guides and Package Vignettes

Read overview or browse directory.

## Help Pages

crlmm-package | Genotype Calling via CRLMM Algorithm
$,CrlmmSetList-method | Class "CrlmmSetList"
A | Class "ABset"
A,ABset-method | Class "ABset"
A,CrlmmSetList-method | Class "CrlmmSetList"
A<- | Class "CrlmmSetList"
A<-,ABset,matrix-method | Class "ABset"
A<-,CrlmmSetList,matrix-method | Class "CrlmmSetList"
ABset-class | Class "ABset"
addFeatureAnnotation | Class "CrlmmSetList"
addFeatureAnnotation,CrlmmSetList-method | Class "CrlmmSetList"
B | Class "ABset"
B,ABset-method | Class "ABset"
B,CrlmmSetList-method | Class "CrlmmSetList"
B<- | Class "CrlmmSetList"
B<-,ABset,matrix-method | Class "ABset"
B<-,CrlmmSetList,matrix-method | Class "CrlmmSetList"
batch | Stores information on the batch (e.g., chemistry plate) used to process samples.
batch,CopyNumberSet-method | Class "CopyNumberSet"
batch,CrlmmSetList-method | Class "CrlmmSetList"
CA | Class "CopyNumberSet"
CA,CopyNumberSet-method | Class "CopyNumberSet"
CA,CrlmmSetList-method | Class "CrlmmSetList"
CA<- | Class "CopyNumberSet"
CA<-,CopyNumberSet,matrix-method | Class "CopyNumberSet"
CA<-,CrlmmSetList,matrix-method | Class "CrlmmSetList"
calls | Accessors for Calls and Confidences on a SnpSet object
calls,CrlmmSetList-method | Class "CrlmmSetList"
calls,SnpSet-method | Accessors for Calls and Confidences on a SnpSet object
CB | Class "CopyNumberSet"
CB,CopyNumberSet-method | Class "CopyNumberSet"
CB,CrlmmSetList-method | Class "CrlmmSetList"
CB<- | Class "CopyNumberSet"
CB<-,CopyNumberSet,matrix-method | Class "CopyNumberSet"
CB<-,CrlmmSetList,matrix-method | Class "CrlmmSetList"
celDates | Extract dates from the cel file header
chromosome | Methods for eSet derivatives
chromosome,CopyNumberSet-method | Class "CopyNumberSet"
chromosome,CrlmmSetList-method | Class "CrlmmSetList"
chromosome,eSet-method | Methods for eSet derivatives
cnIndex | Methods for eSet derivatives
cnIndex,CrlmmSetList-method | Class "CrlmmSetList"
cnIndex,eSet-method | Methods for eSet derivatives
cnrma | Quantile normalizes the intensities for the nonpolymorphic probe to a HapMap reference distribution.
combine,CrlmmSetList,CrlmmSetList-method | Class "CrlmmSetList"
computeCopynumber | Computes copy number
confs | Accessors for Calls and Confidences on a SnpSet object
confs,CrlmmSetList-method | Class "CrlmmSetList"
confs,SnpSet-method | Accessors for Calls and Confidences on a SnpSet object
copyNumber,CopyNumberSet-method | Class "CopyNumberSet"
copyNumber,CrlmmSetList-method | Class "CrlmmSetList"
CopyNumberSet-class | Class "CopyNumberSet"
crlmm | Genotype oligonucleotide arrays with CRLMM
crlmmIllumina | Genotype Illumina Infinium II BeadChip data with CRLMM
CrlmmSetList-class | Class "CrlmmSetList"
crlmmWrapper | Wrapper to quantile normalize and genotype Affymetrix 6.0 cel files.
ellipse,CopyNumberSet-method | Class "CopyNumberSet"
list.celfiles | List CEL files.
ncol,CrlmmSetList-method | Class "CrlmmSetList"
nrow,CrlmmSetList-method | Class "CrlmmSetList"
plot,ABset,CopyNumberSet-method | Class "CopyNumberSet"
plot,CrlmmSetList,ANY-method | Class "CrlmmSetList"
points,CrlmmSetList-method | Class "CrlmmSetList"
position | Methods for eSet derivatives
position,CopyNumberSet-method | Class "CopyNumberSet"
position,CrlmmSetList-method | Class "CrlmmSetList"
position,eSet-method | Methods for eSet derivatives
readIdatFiles | Reads Idat Files from Infinium II Illumina BeadChips
sampleNames,CrlmmSetList-method | Class "CrlmmSetList"
show,CrlmmSetList-method | Class "CrlmmSetList"
snpIndex | Methods for eSet derivatives
snpIndex,CrlmmSetList-method | Class "CrlmmSetList"
snpIndex,eSet-method | Methods for eSet derivatives
snprma | Preprocessing tool for SNP arrays.
update,character-method | Class "CrlmmSetList"
update,CrlmmSetList-method | Class "CrlmmSetList"
[,CrlmmSetList-method | Class "CrlmmSetList"