Man pages for genoset
A RangedSummarizedExperiment with methods for copy number analysis
| baf2mbaf | Calculate mBAF from BAF |
| boundingIndices | Find indices of features bounding a set of chromosome... |
| boundingIndicesByChr | Find indices of features bounding a set of chromosome... |
| bounds2Rle | Convert bounding indices into a Rle |
| calcGC | Calculate GC Percentage in windows |
| calcGC2 | Calculate GC Percentage in sliding window |
| chrIndices-methods | Get a matrix of first and last index of features in each... |
| chrInfo-methods | Get chromosome start and stop positions |
| chr-methods | Chromosome name for each feature |
| chrNames-methods | Get list of unique chromosome names |
| chrOrder | Order chromosome names in proper genome order |
| chrPartitioning | Partitioning by Chromosome |
| cn2lr-methods | Take vector or matrix of copynumber values, convert to... |
| do_rledf_range_summary | Calculate min/max/sum/mean/whichmin/whichmax over ranges on... |
| do_rledf_views | Calculate min/max/sum/mean/whichmin/whichmax over each view... |
| fixSegNAs | Fix NA runs in a Rle |
| gcCorrect | Correct copy number for GC content |
| genome | Get and set the genome universe annotation. |
| genomeAxis | Label axis with base pair units |
| genomicranges-methods | GenomicRanges API Additions |
| genoPlot-methods | Plot data along the genome |
| genoPos-methods | Get base positions of features in genome-scale units |
| GenoSet-class | Class '"GenoSet"' |
| genoset-dataset | Example GenoSet object |
| genoset-methods | Create a GenoSet object |
| genoset-package | GenoSet: An eSet for data with genome locations |
| genoset-subset | Subset a GenoSet |
| isGenomeOrder | Check if a GRanges orGenoSet is in genome order |
| lr2cn | Take vector or matrix of log2 ratios, convert to copynumber |
| modeCenter | Center continuous data on mode |
| numCallable | Count Rle positions >= min |
| pos-methods | Chromosome position of features |
| rangeSampleMeans | Average features in ranges per sample |
| rangeSegMeanLength-methods | Get segment widths |
| rbindDataframe | A fast method for concatenating data.frames |
| readGenoSet | Load a GenoSet from a RData file |
| RleDataFrame-class | Class '"RleDataFrame"' |
| RleDataFrame-views | Calculate summary statistics on views of an RleDataFrame |
| runCBS | Run CBS Segmentation |
| segPairTable-methods | 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-methods | Convert Rle objects to tables of segments |
| toGenomeOrder | Set a GRanges or GenoSet to genome order |
