oligo-package |
The oligo package: a tool for low-level analysis of oligonucleotide arrays |
basecontent |
Sequence Base Contents |
basicRMA |
Simplified Interface to RMA |
bg |
Accessors and replacement methods for the PM/MM/BG matrices. |
bg,FeatureSet-method |
Accessors and replacement methods for the PM/MM/BG matrices. |
bg,TilingFeatureSet2-method |
Accessors and replacement methods for the PM/MM/BG matrices. |
bg<- |
Accessors and replacement methods for the PM/MM/BG matrices. |
bg<-,FeatureSet,matrix-method |
Accessors and replacement methods for the PM/MM/BG matrices. |
bg<-,TilingFeatureSet2,array-method |
Accessors and replacement methods for the PM/MM/BG matrices. |
boxplot |
Boxplot |
boxplot,ExpressionSet-method |
Boxplot |
boxplot,FeatureSet-method |
Boxplot |
cleanPlatformName |
Parser to CEL files |
crlmm |
Genotype Calls |
getContainer |
Get container information for NimbleGen Tiling Arrays. |
getContainer,TilingFeatureSet-method |
Get container information for NimbleGen Tiling Arrays. |
getContainer-methods |
Get container information for NimbleGen Tiling Arrays. |
getCrlmmSummaries |
Function to get CRLMM summaries saved to disk |
getNgsColorsInfo |
Helper function to extract color information for filenames on
NimbleGen arrays. |
getX |
Accessors for physical array coordinates. |
getX,DBPDInfo-method |
Accessors for physical array coordinates. |
getX,FeatureSet-method |
Accessors for physical array coordinates. |
getX-methods |
Accessors for physical array coordinates. |
getY |
Accessors for physical array coordinates. |
getY,DBPDInfo-method |
Accessors for physical array coordinates. |
getY,FeatureSet-method |
Accessors for physical array coordinates. |
getY-methods |
Accessors for physical array coordinates. |
hist |
Density estimate |
hist,ExpressionSet-method |
Density estimate |
hist,FeatureSet-method |
Density estimate |
image |
Display a Color Image |
image,FeatureSet-method |
Display a Color Image |
justCRLMM |
Genotype Calls |
justSNPRMA |
Summarization of SNP data |
list.celfiles |
List CEL/XYS files |
list.xysfiles |
List CEL/XYS files |
MAplot |
MA plots |
MAplot,FeatureSet-method |
MA plots |
MAplot-methods |
MA plots |
mm |
Accessors and replacement methods for the PM/MM/BG matrices. |
mm,FeatureSet-method |
Accessors and replacement methods for the PM/MM/BG matrices. |
mm,TilingFeatureSet2-method |
Accessors and replacement methods for the PM/MM/BG matrices. |
mm<- |
Accessors and replacement methods for the PM/MM/BG matrices. |
mm<-,FeatureSet,matrix-method |
Accessors and replacement methods for the PM/MM/BG matrices. |
mm<-,TilingFeatureSet2,array-method |
Accessors and replacement methods for the PM/MM/BG matrices. |
plotM |
Methods for Log-Ratio plotting |
plotM,SnpQSet,character-method |
Methods for Log-Ratio plotting |
plotM,SnpQSet,integer-method |
Methods for Log-Ratio plotting |
plotM,SnpQSet,numeric-method |
Methods for Log-Ratio plotting |
plotM,TilingQSet,missing-method |
Methods for Log-Ratio plotting |
plotM-methods |
Methods for Log-Ratio plotting |
pm |
Accessors and replacement methods for the PM/MM/BG matrices. |
pm,FeatureSet-method |
Accessors and replacement methods for the PM/MM/BG matrices. |
pm,TilingFeatureSet2-method |
Accessors and replacement methods for the PM/MM/BG matrices. |
pm<- |
Accessors and replacement methods for the PM/MM/BG matrices. |
pm<-,FeatureSet,matrix-method |
Accessors and replacement methods for the PM/MM/BG matrices. |
pm<-,TilingFeatureSet2,array-method |
Accessors and replacement methods for the PM/MM/BG matrices. |
read.celfiles |
Parser to CEL files |
read.celfiles2 |
Parser to CEL files |
read.xysfiles |
Parser to XYS files |
read.xysfiles2 |
Parser to XYS files |
readSummaries |
Read summaries generated by crlmm |
rma |
RMA - Robust Multichip Average algorithm |
rma,ExonFeatureSet-method |
RMA - Robust Multichip Average algorithm |
rma,ExpressionFeatureSet-method |
RMA - Robust Multichip Average algorithm |
rma,GeneFeatureSet-method |
RMA - Robust Multichip Average algorithm |
sequenceDesignMatrix |
Create design matrix for sequences |
snprma |
Preprocessing SNP Arrays |