Tools for low-level analysis of oligonucleotide arrays.


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Documentation for package ‘oligo’ version 1.10.4

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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