# A RangedSummarizedExperiment with methods for copy number analysis

## Documentation for package ‘genoset’ version 1.38.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

genoset-package | GenoSet: An eSet for data with genome locations
as.matrix-method | Class '"RleDataFrame"'
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
chrPartitioning | Partitioning by Chromosome
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"'
colMeans-method | Class '"RleDataFrame"'
colSums-method | Class '"RleDataFrame"'
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
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 object
genoset.ds | Example GenoSet object
GenoSetOrGenomicRanges-class | Class '"GenoSet"'
isGenomeOrder | Check if a GRanges orGenoSet is in genome order
lengths-method | Create a GenoSet object
lr2cn | Take vector or matrix of log2 ratios, convert to copynumber
modeCenter | Center continuous data on mode
nrow-method | GenomicRanges API Additions
numCallable | Count Rle positions >= min
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
rbindDataframe | A fast method for concatenating data.frames
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"'
rowSums-method | Class '"RleDataFrame"'
runCBS | Run CBS Segmentation
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"'
toGenomeOrder | Set a GRanges or GenoSet to genome order
[-method | Subset a GenoSet
[<--method | Subset a GenoSet