A B C D F G H I J L M N O P R S W
oligo-package | The oligo package: a tool for low-level analysis of oligonucleotide arrays |
annotation-method | Class '"oligoPLM"' |
availProbeInfo | Probe information selector. |
backgroundCorrect | Tools for microarray preprocessing. |
backgroundCorrect-method | Tools for microarray preprocessing. |
backgroundCorrect-methods | Tools for microarray preprocessing. |
backgroundCorrectionMethods | Tools for microarray preprocessing. |
basecontent | Sequence Base Contents |
basicPLM | Simplified interface to PLM. |
basicRMA | Simplified interface to RMA. |
bg | Accessors and replacement methods for the intensity/PM/MM/BG matrices. |
bg-method | Accessors and replacement methods for the intensity/PM/MM/BG matrices. |
bg<- | Accessors and replacement methods for the intensity/PM/MM/BG matrices. |
bg<--method | Accessors and replacement methods for the intensity/PM/MM/BG matrices. |
bgindex | Accessors for PM, MM or background probes indices. |
bgindex-method | Accessors for PM, MM or background probes indices. |
bgSequence | Probe Sequeces |
bgSequence-method | Probe Sequeces |
boxplot | Boxplot |
boxplot-method | Boxplot |
boxplot-method | Class '"oligoPLM"' |
boxplot-methods | Boxplot |
chromosome | Accessor for chromosome information |
chromosome<- | Accessor for chromosome information |
chromosome<--method | Accessor for chromosome information |
cleanPlatformName | Parser to CEL files |
coef-method | Class '"oligoPLM"' |
coefs | Defunct Functions in Package 'oligo' |
coefs.probe | Class '"oligoPLM"' |
coefs.probe-method | Class '"oligoPLM"' |
crlmm | Genotype Calls |
darkColors | Create set of colors, interpolating through a set of preferred colors. |
divColors | Create set of colors, interpolating through a set of preferred colors. |
fitPLM | Defunct Functions in Package 'oligo' |
fitProbeLevelModel | Tool to fit Probe Level Models. |
geometry-method | Class '"oligoPLM"' |
getAffinitySplineCoefficients | Estimate affinity coefficients. |
getBaseProfile | Compute and plot nucleotide profile. |
getContainer | Get container information for NimbleGen Tiling Arrays. |
getContainer-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 |
getNetAffx | NetAffx Biological Annotations |
getNetAffx-method | NetAffx Biological Annotations |
getNetAffx-methods | NetAffx Biological Annotations |
getNgsColorsInfo | Helper function to extract color information for filenames on NimbleGen arrays. |
getPD | Retrieve Platform Design object |
getPlatformDesign | Retrieve Platform Design object |
getPlatformDesign-method | Retrieve Platform Design object |
getProbeInfo | Probe information selector. |
getX | Accessors for physical array coordinates. |
getX-method | Accessors for physical array coordinates. |
getX-methods | Accessors for physical array coordinates. |
getY | Accessors for physical array coordinates. |
getY-method | Accessors for physical array coordinates. |
getY-methods | Accessors for physical array coordinates. |
hist | Density estimate |
hist-method | Density estimate |
hist-methods | Density estimate |
image | Display a pseudo-image of a microarray chip |
image-method | Display a pseudo-image of a microarray chip |
image-method | Class '"oligoPLM"' |
image-methods | Display a pseudo-image of a microarray chip |
intensity | Accessors and replacement methods for the intensity/PM/MM/BG matrices. |
intensity-method | Accessors and replacement methods for the intensity/PM/MM/BG matrices. |
intensity<- | Accessors and replacement methods for the intensity/PM/MM/BG matrices. |
intensity<--method | Accessors and replacement methods for the intensity/PM/MM/BG matrices. |
justCRLMM | Genotype Calls |
justSNPRMA | Summarization of SNP data |
list.xysfiles | List XYS files |
manufacturer-method | Class '"oligoPLM"' |
MAplot | MA plots |
MAplot-method | MA plots |
MAplot-methods | MA plots |
method | Class '"oligoPLM"' |
method-method | Class '"oligoPLM"' |
mm | Accessors and replacement methods for the intensity/PM/MM/BG matrices. |
mm-method | Accessors and replacement methods for the intensity/PM/MM/BG matrices. |
mm<- | Accessors and replacement methods for the intensity/PM/MM/BG matrices. |
mm<--method | Accessors and replacement methods for the intensity/PM/MM/BG matrices. |
mmindex | Accessors for PM, MM or background probes indices. |
mmindex-method | Accessors for PM, MM or background probes indices. |
mmSequence | Probe Sequeces |
mmSequence-method | Probe Sequeces |
ncol-method | Class '"oligoPLM"' |
normalizationMethods | Tools for microarray preprocessing. |
normalize-method | Tools for microarray preprocessing. |
normalizeToTarget | Tools for microarray preprocessing. |
normalizeToTarget-method | Tools for microarray preprocessing. |
normalizeToTarget-methods | Tools for microarray preprocessing. |
nprobes | Class '"oligoPLM"' |
nprobes-method | Class '"oligoPLM"' |
nprobesets | Class '"oligoPLM"' |
nprobesets-method | Class '"oligoPLM"' |
NUSE | Class '"oligoPLM"' |
NUSE-method | Class '"oligoPLM"' |
oligo-defunct | Defunct Functions in Package 'oligo' |
oligoPLM | Class '"oligoPLM"' |
oligoPLM-class | Class '"oligoPLM"' |
opset2eset | Class '"oligoPLM"' |
opset2eset-method | Class '"oligoPLM"' |
paCalls | Methods for P/A Calls |
paCalls-method | Methods for P/A Calls |
plotM | Methods for Log-Ratio plotting |
plotM-method | Methods for Log-Ratio plotting |
plotM-methods | Methods for Log-Ratio plotting |
pm | Accessors and replacement methods for the intensity/PM/MM/BG matrices. |
pm-method | Accessors and replacement methods for the intensity/PM/MM/BG matrices. |
pm<- | Accessors and replacement methods for the intensity/PM/MM/BG matrices. |
pm<--method | Accessors and replacement methods for the intensity/PM/MM/BG matrices. |
pmAllele | Access the allele information for PM probes. |
pmAllele-method | Access the allele information for PM probes. |
pmChr | Accessor for chromosome information |
pmChr-method | Accessor for chromosome information |
pmFragmentLength | Access the fragment length for PM probes. |
pmFragmentLength-method | Access the fragment length for PM probes. |
pmindex | Accessors for PM, MM or background probes indices. |
pmindex-method | Accessors for PM, MM or background probes indices. |
pmOffset | Accessor to position information |
pmOffset-method | Accessor to position information |
pmPosition | Accessor to position information |
pmPosition-method | Accessor to position information |
pmSequence | Probe Sequeces |
pmSequence-method | Probe Sequeces |
pmStrand | Accessor to the strand information |
pmStrand-method | Accessor to the strand information |
probeNames | Accessor to feature names |
probeNames-method | Accessor to feature names |
probesetNames | Accessor to feature names |
probesetNames-method | Accessor to feature names |
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 |
resids | Defunct Functions in Package 'oligo' |
residuals-method | Class '"oligoPLM"' |
residualSE | Class '"oligoPLM"' |
residualSE-method | Class '"oligoPLM"' |
RLE | Class '"oligoPLM"' |
RLE-method | Class '"oligoPLM"' |
rma | RMA - Robust Multichip Average algorithm |
rma-method | RMA - Robust Multichip Average algorithm |
rma-methods | RMA - Robust Multichip Average algorithm |
runDate | Date of scan |
runDate-method | Date of scan |
runDate-methods | Date of scan |
se | Class '"oligoPLM"' |
se-method | Class '"oligoPLM"' |
se.probe | Class '"oligoPLM"' |
se.probe-method | Class '"oligoPLM"' |
seqColors | Create set of colors, interpolating through a set of preferred colors. |
seqColors2 | Create set of colors, interpolating through a set of preferred colors. |
sequenceDesignMatrix | Create design matrix for sequences |
show-method | Class '"oligoPLM"' |
snprma | Preprocessing SNP Arrays |
summarizationMethods | Tools for microarray preprocessing. |
summarize | Tools for microarray preprocessing. |
summarize-method | Tools for microarray preprocessing. |
summarize-methods | Tools for microarray preprocessing. |
weights-method | Class '"oligoPLM"' |