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" |