A B C D E F G H I K L M N O P R S T misc
oligo-package | The oligo package: a tool for analysis of oligonucleotide arrays |
$,platformDesign-method | Internals |
AffySNPPDInfo-class | Class "DBPDInfo" |
antisenseThetaA | Summarized Measures for SNP |
antisenseThetaA,SnpQSet-method | Summarized Measures for SNP |
antisenseThetaB | Summarized Measures for SNP |
antisenseThetaB,SnpQSet-method | Summarized Measures for SNP |
basecontent | Sequence Base Contents |
boxplot | Boxplot |
boxplot,FeatureSet-method | Boxplot |
calls | Accessors for SnpCallSet |
calls,SnpCallSet-method | Accessors for SnpCallSet |
calls<-,SnpCallSet,matrix-method | Accessors for SnpCallSet |
callsConfidence | Accessors for SnpCallSet |
callsConfidence,SnpCallSet-method | Accessors for SnpCallSet |
callsConfidence<-,SnpCallSet,matrix-method | Accessors for SnpCallSet |
chromosome | Accessor for chromosome information |
chromosome,TilingFeatureSet-method | Accessor for chromosome information |
cleanPlatformName | Parser to CEL files |
cnConfidence | Accessors for SnpCopyNumberSet objects |
cnConfidence,SnpCopyNumberSet-method | Accessors for SnpCopyNumberSet objects |
cnConfidence<-,SnpCopyNumberSet,matrix-method | Accessors for SnpCopyNumberSet objects |
copyNumber | Accessors for SnpCopyNumberSet objects |
copyNumber,SnpCopyNumberSet-method | Accessors for SnpCopyNumberSet objects |
copyNumber<-,SnpCopyNumberSet,matrix-method | Accessors for SnpCopyNumberSet objects |
crlmm | Genotype Calls |
db | Internals |
db,DBPDInfo-method | Internals |
DBPDInfo-class | Class "DBPDInfo" |
ExonFeatureSet-class | "FeatureSet" Extensions |
ExpressionFeatureSet-class | "FeatureSet" Extensions |
exprs,FeatureSet-method | Internals |
featureIndex | Indexes for features in the expression matrix |
featureIndex,FeatureSet-method | Indexes for features in the expression matrix |
featureInfo | Internals |
featureInfo,platformDesign-method | Internals |
FeatureSet-class | Classes for Feature level data |
geneNames,AffySNPPDInfo-method | Internals |
geneNames,FeatureSet-method | Internals |
geneNames,platformDesign-method | Internals |
genomeBuild | Genome Build Information |
genomeBuild,PDInfo-method | Genome Build Information |
genomeBuild,TilingFeatureSet-method | Genome Build Information |
geometry | List fields in the (pm/mm)feature table |
geometry,PDInfo-method | List fields in the (pm/mm)feature table |
getA | Compute average log-intensities / log-ratios |
getA,SnpQSet-method | Compute average log-intensities / log-ratios |
getChrXIndex | Internals |
getGenotypeRegionParams | Internals |
getM | Compute average log-intensities / log-ratios |
getM,SnpQSet-method | Compute average log-intensities / log-ratios |
getPD | Retrieve Platform Design object |
getPlatformDesign | Retrieve Platform Design object |
getPlatformDesign,FeatureSet-method | Retrieve Platform Design object |
getSnpFragmentLength | Internals |
hist | Density estimate |
hist,FeatureSet-method | Density estimate |
image | Display a Color Image |
image,FeatureSet-method | Display a Color Image |
initialize,DBPDInfo-method | Internals |
initialize,FeatureSet-method | Internals |
initialize,SnpCallSet-method | Internals |
initialize,SnpCopyNumberSet-method | Internals |
initialize,SnpQSet-method | Internals |
kind | Array type |
kind,AffySNPPDInfo-method | Array type |
kind,platformDesign-method | Array type |
length,FeatureSet-method | Internals |
list.celfiles | List CEL/XYS files |
list.xysfiles | List CEL/XYS files |
listFeatureFields | List fields in the (pm/mm)feature table |
listFeatureFields,AffySNPPDInfo-method | List fields in the (pm/mm)feature table |
listFeatureFields,PDInfo-method | List fields in the (pm/mm)feature table |
listFeatureSetFields | List fields in the (pm/mm)feature table |
listFeatureSetFields,AffySNPPDInfo-method | List fields in the (pm/mm)feature table |
listFeatureSetFields,PDInfo-method | List fields in the (pm/mm)feature table |
manufacturer | Accessor to the manufacturer slot. |
manufacturer,FeatureSet-method | Accessor to the manufacturer slot. |
manufacturer,PDInfo-method | Accessor to the manufacturer slot. |
manufacturer<-,FeatureSet-method | Accessor to the manufacturer slot. |
mm | Accessor to the PM/MM matrices |
mm,FeatureSet-method | Accessor to the PM/MM matrices |
mm<-,FeatureSet,BufferedMatrix-method | Accessor to the PM/MM matrices |
mm<-,FeatureSet,matrix-method | Accessor to the PM/MM matrices |
mmindex | Extract PM or MM indexes |
mmindex,AffySNPPDInfo-method | Extract PM or MM indexes |
mmindex,FeatureSet-method | Extract PM or MM indexes |
mmindex,platformDesign-method | Extract PM or MM indexes |
mmSequence | Probe Sequeces |
mmSequence,AffySNPPDInfo-method | Probe Sequeces |
mmSequence,FeatureSet-method | Probe Sequeces |
mmSequence,platformDesign-method | Probe Sequeces |
names,platformDesign-method | Internals |
ncol | ~~function to do ... ~~ |
ncol,platformDesign-method | ~~function to do ... ~~ |
normalizeToSample | Internals |
nProbes | Count number of probes |
nProbes,AffySNPPDInfo-method | Count number of probes |
nProbes,platformDesign-method | Count number of probes |
nrow | ~~function to do ... ~~ |
nrow,platformDesign-method | ~~function to do ... ~~ |
oligoSnpSet-class | "SnpSet" Extensions |
PDInfo-class | Classes "PDInfo" and "SNPPDInfo" |
platform | Retrieve/replace platform information |
platform,FeatureSet-method | Retrieve/replace platform information |
platform<-,FeatureSet-method | Retrieve/replace platform information |
platformDesign-class | Class "platformDesign" |
platformDesignName | Internals |
platformDesignName,FeatureSet-method | Internals |
plotDensity | Plot density of intensities. |
pm | Accessor to the PM/MM matrices |
pm,FeatureSet-method | Accessor to the PM/MM matrices |
pm<-,FeatureSet,BufferedMatrix-method | Accessor to the PM/MM matrices |
pm<-,FeatureSet,matrix-method | Accessor to the PM/MM matrices |
pmAllele | Access the allele information for PM probes. |
pmAllele,AffySNPPDInfo-method | Access the allele information for PM probes. |
pmAllele,PDInfo-method | Access the allele information for PM probes. |
pmAllele,SnpFeatureSet-method | Access the allele information for PM probes. |
pmChr | Accessor for chromosome information |
pmChr,TilingFeatureSet-method | Accessor for chromosome information |
pmindex | Extract PM or MM indexes |
pmindex,AffySNPPDInfo-method | Extract PM or MM indexes |
pmindex,FeatureSet-method | Extract PM or MM indexes |
pmindex,platformDesign-method | Extract PM or MM indexes |
pmPosition | Accessor to position information |
pmPosition,AffySNPPDInfo-method | Accessor to position information |
pmPosition,TilingFeatureSet-method | Accessor to position information |
pmSequence | Probe Sequeces |
pmSequence,AffySNPPDInfo-method | Probe Sequeces |
pmSequence,FeatureSet-method | Probe Sequeces |
pmSequence,platformDesign-method | Probe Sequeces |
pmStrand | Accessor to the strand information |
pmStrand,AffySNPPDInfo-method | Accessor to the strand information |
position | Accessor to position information |
position,TilingFeatureSet-method | Accessor to position information |
probeNames | Accessor to feature names |
probeNames,AffySNPPDInfo-method | Accessor to feature names |
probeNames,FeatureSet-method | Accessor to feature names |
probeNames,platformDesign-method | Accessor to feature names |
read.celfiles | Parser to CEL files |
read.xysfiles | Parser to XYS files |
rma | RMA |
rma,FeatureSet-method | RMA |
senseThetaA | Summarized Measures for SNP |
senseThetaA,SnpQSet-method | Summarized Measures for SNP |
senseThetaB | Summarized Measures for SNP |
senseThetaB,SnpQSet-method | Summarized Measures for SNP |
sequenceDesignMatrix | Create design matrix for sequences |
show,PDInfo-method | Internals |
show,platformDesign-method | Internals |
SnpCallSet-class | "SnpSet" Extensions |
SnpCopyNumberSet-class | "SnpSet" Extensions |
SnpFeatureSet-class | "FeatureSet" Extensions |
SNPPDInfo-class | Classes "PDInfo" and "SNPPDInfo" |
SnpQSet-class | Class "SnpQSet" |
snprma | Preprocessing SNP Arrays |
TilingFeatureSet-class | "FeatureSet" Extensions |
[,FeatureSet-method | Internals |