Man pages for acidgenomics/r-acidexperiment
Acid Genomics Summarized Experiment
| AcidExperiment-package | AcidExperiment |
| AcidExperimentTestsURL | AcidExperiment test data URL |
| aggregate | Aggregate |
| as.SummarizedExperiment | Coerce to 'SummarizedExperiment'. |
| autopadZeros | Autopad zeros |
| calculateMetrics | Calculate quality control metrics |
| combine | Combine multiple objects |
| convertGenesToSymbols | Convert genes to symbols |
| convertSampleIDsToNames | Convert sample identifiers to names |
| convertTranscriptsToGenes | Convert transcripts to genes |
| correlation | Correlation |
| counts | Counts |
| decode | Decode column data that uses run-length encoding |
| defunct | Defunct functions |
| detectLanes | Detect sequencing lanes |
| droplevels2 | Drop unused levels from factors |
| encode | Encode using run-length encoding |
| Ensembl2Entrez | Ensembl-to-Entrez gene identifier mappings |
| estimateSizeFactors | Estimate size factors |
| export | Export |
| Gene2Symbol | Gene-to-symbol mappings |
| geneNames | Gene names |
| headtail | Return the first and last parts of an object |
| humanize | Humanize an R object |
| importSampleData | Import sample metadata |
| integerCounts | Integer counts |
| interestingGroups | Interesting groups |
| makeSampleData | Make sample data |
| makeSummarizedExperiment | Make a SummarizedExperiment object |
| mapGenes | Map genes |
| matchInterestingGroups | Match interesting groups |
| matchSampleColumn | Match sample identifier column |
| melt | Melt columns into key-value pairs |
| metrics | Quality control metrics |
| microplate | Microtiter plate well identifiers |
| minimalSampleData | Minimal sample data |
| nonzeroRowsAndCols | Subset object to keep only non-zero rows and columns |
| organism | Organism |
| sampleData | Sample data |
| sampleNames | Sample names |
| sanitizeSampleData | Sanitize sample data |
| selectSamples | Select samples |
| sizeFactors | Size factors |
| stripGeneVersions | Strip gene identifier versions |
| stripTranscriptVersions | Strip transcript identifier versions |
| syntactic | Syntactic naming functions |
| tpm | Transcripts per million |
| Tx2Gene | Transcript-to-gene mappings |
| uniteInterestingGroups | Unite interesting groups into a single column |
