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"' |