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


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Documentation for package ‘crlmm’ version 1.4.5

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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"