Entry: mm
Aliases: mm pm bg mm,FeatureSet-method pm,FeatureSet-method bg,FeatureSet-method mm,TilingFeatureSet2-method pm,TilingFeatureSet2-method bg,TilingFeatureSet2-method mm<- pm<- bg<- mm<-,FeatureSet,matrix-method pm<-,FeatureSet,matrix-method bg<-,FeatureSet,matrix-method mm<-,TilingFeatureSet2,array-method pm<-,TilingFeatureSet2,array-method bg<-,TilingFeatureSet2,array-method
Keywords: manip
Description: Accessors and replacement methods for the PM/MM/BG matrices.
URL: ../../../library/oligo/html/IntensityMatrix-methods.html

Entry: MAplot-methods
Aliases: MAplot MAplot-methods MAplot,FeatureSet-method
Keywords: methods
Description: MA plots
URL: ../../../library/oligo/html/MAplot-methods.html

Entry: basecontent
Aliases: basecontent
Keywords: manip
Description: Sequence Base Contents
URL: ../../../library/oligo/html/basecontent.html

Entry: basicRMA
Aliases: basicRMA
Keywords: manip
Description: Simplified Interface to RMA
URL: ../../../library/oligo/html/basicRMA.html

Entry: boxplot
Aliases: boxplot boxplot,FeatureSet-method boxplot,ExpressionSet-method
Keywords: hplot
Description: Boxplot
URL: ../../../library/oligo/html/boxplot.html

Entry: getX
Aliases: getX getY getX-methods getX,FeatureSet-method getX,DBPDInfo-method getY-methods getY,FeatureSet-method getY,DBPDInfo-method
Keywords: manip
Description: Accessors for physical array coordinates.
URL: ../../../library/oligo/html/coordinates.html

Entry: crlmm
Aliases: crlmm justCRLMM
Keywords: classif
Description: Genotype Calls
URL: ../../../library/oligo/html/crlmm.html

Entry: getContainer
Aliases: getContainer getContainer-methods getContainer,TilingFeatureSet-method
Keywords: manip
Description: Get container information for NimbleGen Tiling Arrays.
URL: ../../../library/oligo/html/getContainer.html

Entry: getCrlmmSummaries
Aliases: getCrlmmSummaries
Keywords: manip
Description: Function to get CRLMM summaries saved to disk
URL: ../../../library/oligo/html/getCrlmmSummaries.html

Entry: getNgsColorsInfo
Aliases: getNgsColorsInfo
Keywords: manip
Description: Helper function to extract color information for filenames on NimbleGen arrays.
URL: ../../../library/oligo/html/getNgsColorsInfo.html

Entry: hist
Aliases: hist hist,FeatureSet-method hist,ExpressionSet-method
Keywords: hplot
Description: Density estimate
URL: ../../../library/oligo/html/hist.html

Entry: image
Aliases: image image,FeatureSet-method
Keywords: hplot
Description: Display a Color Image
URL: ../../../library/oligo/html/image.html

Entry: justSNPRMA
Aliases: justSNPRMA
Keywords: manip
Description: Summarization of SNP data
URL: ../../../library/oligo/html/justSNPRMA.html

Entry: list.celfiles
Aliases: list.celfiles list.xysfiles
Keywords: file
Description: List CEL/XYS files
URL: ../../../library/oligo/html/list.celfiles.html

Entry: oligo-package
Aliases: oligo-package
Keywords: package
Description: The oligo package: a tool for low-level analysis of oligonucleotide arrays
URL: ../../../library/oligo/html/oligo-package.html

Entry: plotM-methods
Aliases: plotM plotM-methods plotM,SnpQSet,character-method plotM,SnpQSet,integer-method plotM,SnpQSet,numeric-method plotM,TilingQSet,missing-method
Keywords: methods
Description: Methods for Log-Ratio plotting
URL: ../../../library/oligo/html/plotM-methods.html

Entry: read.celfiles
Aliases: read.celfiles read.celfiles2 cleanPlatformName
Keywords: IO
Description: Parser to CEL files
URL: ../../../library/oligo/html/read.celfiles.html

Entry: read.xysfiles
Aliases: read.xysfiles read.xysfiles2
Keywords: IO
Description: Parser to XYS files
URL: ../../../library/oligo/html/read.xysfiles.html

Entry: readSummaries
Aliases: readSummaries
Keywords: manip
Description: Read summaries generated by crlmm
URL: ../../../library/oligo/html/readSummaries.html

Entry: rma
Aliases: rma rma,ExpressionFeatureSet-method rma,ExonFeatureSet-method rma,GeneFeatureSet-method
Keywords: manip
Description: RMA - Robust Multichip Average algorithm
URL: ../../../library/oligo/html/rma.html

Entry: sequenceDesignMatrix
Aliases: sequenceDesignMatrix
Keywords: manip
Description: Create design matrix for sequences
URL: ../../../library/oligo/html/sequenceDesignMatrix.html

Entry: snprma
Aliases: snprma
Keywords: manip
Description: Preprocessing SNP Arrays
URL: ../../../library/oligo/html/snprma.html
