# Tools for low-level analysis of oligonucleotide arrays.

## Documentation for package ‘oligo’ version 1.10.4

## User Guides and Package Vignettes

Read overview or browse directory.

## Help Pages

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