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A B C D E F G I L M N P R S T W misc
| genoset-package | GenoSet: An eSet for data with genome locations |
| API | Converting eSet API to RangedSummarizedExperiment |
| as.matrix-method | Class '"RleDataFrame"' |
| assay-method | Converting eSet API to RangedSummarizedExperiment |
| assay<--method | Converting eSet API to RangedSummarizedExperiment |
| assayNames-method | Converting eSet API to RangedSummarizedExperiment |
| assays-method | Converting eSet API to RangedSummarizedExperiment |
| baf2mbaf | Calculate mBAF from BAF |
| boundingIndices | Find indices of features bounding a set of chromosome ranges/genes |
| boundingIndicesByChr | Find indices of features bounding a set of chromosome ranges/genes, across chromosomes |
| bounds2Rle | Convert bounding indices into a Rle |
| calcGC | Calculate GC Percentage in windows |
| calcGC2 | Calculate GC Percentage in sliding window |
| chr | Chromosome name for each feature |
| chr-method | Chromosome name for each feature |
| chrIndices | Get a matrix of first and last index of features in each chromosome |
| chrIndices-method | Get a matrix of first and last index of features in each chromosome |
| chrInfo | Get chromosome start and stop positions |
| chrInfo-method | Get chromosome start and stop positions |
| chrNames | Get list of unique chromosome names |
| chrNames-method | Get list of unique chromosome names |
| chrNames<- | Get list of unique chromosome names |
| chrNames<--method | Get list of unique chromosome names |
| chrOrder | Order chromosome names in proper genome order |
| cn2lr | Take vector or matrix of copynumber values, convert to log2ratios |
| cn2lr-method | Take vector or matrix of copynumber values, convert to log2ratios |
| coerce-method | Class '"RleDataFrame"' |
| colData-method | Converting eSet API to RangedSummarizedExperiment |
| colMeans-method | Class '"RleDataFrame"' |
| colnames-method | Get colnames from a GenoSet |
| colnames<--method | Get colnames from a GenoSet |
| colSums-method | Class '"RleDataFrame"' |
| dim-method | Dimensions |
| elementLengths-method | Get elementLengths from locData slot |
| end-method | Get end of location for each feature |
| fake.baf | Example GenoSet, BAFSet, and CNSet objects and the data to create them. |
| fake.cn | Example GenoSet, BAFSet, and CNSet objects and the data to create them. |
| fake.lrr | Example GenoSet, BAFSet, and CNSet objects and the data to create them. |
| fake.pData | Example GenoSet, BAFSet, and CNSet objects and the data to create them. |
| featureNames-method | Get rownames from GRanges, or GenoSet |
| featureNames<--method | Get rownames from GRanges, or GenoSet |
| fixSegNAs | Fix NA runs in a Rle |
| gcCorrect | Correct copy number for GC content |
| genome | Get and set the genome universe annotation. |
| genome-method | Genome version |
| genome<--method | Genome version |
| genomeAxis | Label axis with base pair units |
| genoPlot | Plot data along the genome |
| genoPlot-method | Plot data along the genome |
| genoPos | Get base positions of features in genome-scale units |
| genoPos-method | Get base positions of features in genome-scale units |
| GenoSet | Create a GenoSet object |
| genoset | GenoSet: An eSet for data with genome locations |
| GenoSet-class | Class '"GenoSet"' |
| genoset-datasets | Example GenoSet, BAFSet, and CNSet objects and the data to create them. |
| genoset-defunct | Defunct genoset features |
| genoset-deprecated | Deprecated genoset features |
| genoset.ds | Example GenoSet, BAFSet, and CNSet objects and the data to create them. |
| GenoSetOrGenomicRanges-class | Class '"GenoSet"' |
| initGenoSet | Create a GenoSet or derivative object |
| isGenomeOrder | Check if a GRanges orGenoSet is in genome order |
| isGenomeOrder-method | Check if a GRanges orGenoSet is in genome order |
| locData | Access the feature genome position info |
| locData-method | Access the feature genome position info |
| locData.gr | Example GenoSet, BAFSet, and CNSet objects and the data to create them. |
| locData<- | Access the feature genome position info |
| locData<--method | Access the feature genome position info |
| lr2cn | Take vector or matrix of log2 ratios, convert to copynumber |
| modeCenter | Center continuous data on mode |
| names-method | Get data matrix names |
| nrow-method | Number of rows |
| nrow-method | Number of rows |
| numCallable | Count Rle positions >= min |
| pData-method | Converting eSet API to RangedSummarizedExperiment |
| pos | Chromosome position of features |
| pos-method | Chromosome position of features |
| rangeColMeans | Calculate summary statistics on views of an RleDataFrame |
| rangeMaxs | Calculate summary statistics on views of an RleDataFrame |
| rangeMaxs-method | Calculate summary statistics on views of an RleDataFrame |
| rangeMeans | Calculate summary statistics on views of an RleDataFrame |
| rangeMeans-method | Calculate summary statistics on views of an RleDataFrame |
| rangeMins | Calculate summary statistics on views of an RleDataFrame |
| rangeMins-method | Calculate summary statistics on views of an RleDataFrame |
| rangeSampleMeans | Average features in ranges per sample |
| rangeSegMeanLength | Get segment widths |
| rangeSegMeanLength-method | Get segment widths |
| rangeSums | Calculate summary statistics on views of an RleDataFrame |
| rangeSums-method | Calculate summary statistics on views of an RleDataFrame |
| rangeWhichMaxs | Calculate summary statistics on views of an RleDataFrame |
| rangeWhichMaxs-method | Calculate summary statistics on views of an RleDataFrame |
| rangeWhichMins | Calculate summary statistics on views of an RleDataFrame |
| rangeWhichMins-method | Calculate summary statistics on views of an RleDataFrame |
| readGenoSet | Load a GenoSet from a RData file |
| RleDataFrame | Class '"RleDataFrame"' |
| RleDataFrame-class | Class '"RleDataFrame"' |
| RleDataFrame-views | Calculate summary statistics on views of an RleDataFrame |
| rowMeans-method | Class '"RleDataFrame"' |
| rownames-method | Get rownames from GRanges, or GenoSet |
| rownames<--method | Get rownames from GRanges, or GenoSet |
| rowRanges-method | Access the feature genome position info |
| rowSums-method | Class '"RleDataFrame"' |
| runCBS | Run CBS Segmentation |
| sampleNames-method | Get colnames from a GenoSet |
| sampleNames<--method | Get colnames from a GenoSet |
| segPairTable | Convert Rle objects to tables of segments |
| segPairTable-method | Convert Rle objects to tables of segments |
| segs2Granges | GRanges from segment table |
| segs2Rle | Make Rle from segments for one sample |
| segs2RleDataFrame | CBS segments to probe matrix |
| segTable | Convert Rle objects to tables of segments |
| segTable-method | Convert Rle objects to tables of segments |
| show-method | Class '"RleDataFrame"' |
| show-method | Print a GenoSet |
| start-method | Get start of location for each feature |
| subsetAssayData | Subset or re-order assayData |
| toGenomeOrder | Set a GRanges or GenoSet to genome order |
| toGenomeOrder-method | Set a GRanges or GenoSet to genome order |
| width-method | Get width of location for each feature |
| [-method | Subset a GenoSet |
| [<--method | Subset a GenoSet |