Man pages for NeilPearson-Lilly/MethyLiution
MethyLiution: A QC Pipeline For Methylation Data
| checkReportedSex | Step 3: Check that metadata for samples matches inferences |
| chooseBestArray | Step 4: Where multiple arrays are present for some samples,... |
| cite_me | Cite MethyLiution |
| colourAdjustment | Step 6: Colour balancing for 2-colour microarrays Applies a... |
| detectOutliers | Step 5: Detect (but do not remove) outliers Makes a... |
| findSurrogateVariables | Step 10: Apply surrogate variable analysis to automatically... |
| normalisation | Step 7: Apply inter-assay normalisation Apply a broader... |
| probe_data | Filtered probe lists for EPIC and 450K datasets |
| quantileNormalisation | Step 8: Apply Beta-Mixture Quantile normalisation, producing... |
| readData | Step 1: Read dataset files |
| removeAssaysWithMissingMetadata | Step 9: Remove assays with missing metadata |
| removeSnpProbesAndImprintingGenes | Step 2: Filter SNP probes and imprinting genes |
| runPipeline | runPipeline |
| setColumnNames | Set column names |
