Man pages for benilton/oligoOld
Preprocessing tools for oligonucleotide arrays
| basecontent | Sequence Base Contents |
| basicPLM | Simplified interface to PLM. |
| basicRMA | Simplified interface to RMA. |
| boxplot | Boxplot |
| chromosome | Accessor for chromosome information |
| colors | Create set of colors, interpolating through a set of... |
| coordinates | Accessors for physical array coordinates. |
| crlmm | Genotype Calls |
| fitProbeLevelModel | Tool to fit Probe Level Models. |
| getAffinitySplineCoefficients | Estimate affinity coefficients. |
| getBaseProfile | Compute and plot nucleotide profile. |
| getContainer | Get container information for NimbleGen Tiling Arrays. |
| getCrlmmSummaries | Function to get CRLMM summaries saved to disk |
| getNetAffx | NetAffx Biological Annotations |
| getNgsColorsInfo | Helper function to extract color information for filenames on... |
| getPlatformDesign | Retrieve Platform Design object |
| getProbeInfo | Probe information selector. |
| hist | Density estimate |
| image | Display a pseudo-image of a microarray chip |
| Index-methods | Accessors for PM, MM or background probes indices. |
| IntensityMatrix-methods | Accessors and replacement methods for the intensity/PM/MM/BG... |
| justSNPRMA | Summarization of SNP data |
| list.xysfiles | List XYS files |
| MAplot-methods | MA plots |
| oligoDefunct | Defunct Functions in Package 'oligo' |
| oligo-package | The oligo package: a tool for low-level analysis of... |
| oligoPLM-class | Class '"oligoPLM"' |
| paCalls | Methods for P/A Calls |
| plotM-methods | Methods for Log-Ratio plotting |
| pmAllele | Access the allele information for PM probes. |
| pmFragmentLength | Access the fragment length for PM probes. |
| pmPosition | Accessor to position information |
| pmStrand | Accessor to the strand information |
| preprocessTools | Tools for microarray preprocessing. |
| probeNames | Accessor to feature names |
| read.celfiles | Parser to CEL files |
| readSummaries | Read summaries generated by crlmm |
| read.xysfiles | Parser to XYS files |
| rma-methods | RMA - Robust Multichip Average algorithm |
| runDate | Date of scan |
| sequenceDesignMatrix | Create design matrix for sequences |
| Sequences-methods | Probe Sequeces |
| snprma | Preprocessing SNP Arrays |
